bio
AlphaFold
https://deepmind.com/research/case-studies/alphafold
Package description
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
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AlphaLink
https://github.com/lhatsk/AlphaLink
Package description
AlphaLink predicts protein structures using deep learning given a sequence and a set of experimental contacts. It extends OpenFold with crosslinking MS data or other experimental distance restraint by explicitly incorporating them in the OpenFold architecture.
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BCFtools
Package description
Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
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BCL
http://www.meilerlab.org/index.php/bclcommons/show/b_apps_id/1
Package description
The Bio Chemical Library (BCL) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data. The BCL contains the widely used secondary structure prediction program JUFO, a folding algorithm that assembles secondary structure elements, and loop construction tools that complete protein backbones.
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BEDOPS
http://bedops.readthedocs.io/en/latest/index.html
Package description
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
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BEDTools
https://bedtools.readthedocs.io/
Package description
BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
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BLAST
http://blast.ncbi.nlm.nih.gov/
Package description
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
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BLAST+
https://blast.ncbi.nlm.nih.gov/
Package description
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
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BWA
http://bio-bwa.sourceforge.net/
Package description
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
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BamTools
https://github.com/pezmaster31/bamtools
Package description
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
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Beagle
https://faculty.washington.edu/browning/beagle/beagle.html
Package description
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
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Beast
Package description
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
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Bio-DB-HTS
https://metacpan.org/release/Bio-DB-HTS
Package description
Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
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BioPerl
Package description
Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
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Biopython
Package description
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
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Bowtie
http://bowtie-bio.sourceforge.net/index.shtml
Package description
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
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Bowtie2
https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Package description
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
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CNVkit
https://github.com/etal/cnvkit
Package description
A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
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Clustal-Omega
Package description
Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
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ClustalW2
https://www.ebi.ac.uk/Tools/msa/clustalw2/
Package description
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
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Crumble
https://github.com/jkbonfield/crumble
Package description
Exploration of controlled loss of quality values for compressing CRAM files
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DROP
https://gagneurlab-drop.readthedocs.io
Package description
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
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ExpansionHunter
https://github.com/Illumina/ExpansionHunter
Package description
There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. Fragile X Syndrome, ALS, and Huntington's Disease are well known examples. Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for reads that span, flank, and are fully contained in each repeat.
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FastQC
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Package description
FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
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GATK
https://www.broadinstitute.org/gatk/
Package description
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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GCTA
https://yanglab.westlake.edu.cn/software/gcta/
Package description
GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs).
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GRIDSS
https://github.com/PapenfussLab/gridss
Package description
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
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GROMACS
Package description
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. It also contains the gmxapi extension for the single precision MPI build next to PLUMED.
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GView
https://github.com/phac-nml/gview-wiki/wiki
Package description
GView is a Java package used to display and navigate bacterial genomes.
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HH-suite
https://github.com/soedinglab/hh-suite
Package description
The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
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HISAT2
https://daehwankimlab.github.io/hisat2
Package description
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
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HMMER
Package description
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
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HTSlib
Package description
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
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HiCExplorer
http://hicexplorer.readthedocs.org/
Package description
HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.
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HiCMatrix
https://github.com/deeptools/HiCMatrix
Package description
This library implements the central class of HiCExplorer to manage Hi-C interaction matrices.
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IQ-Tree
Package description
Efficient and versatile phylogenomic software by maximum likelihood
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Infernal
Package description
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.
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Iris
https://github.com/mkirsche/Iris
Package description
A module for improving the insertion sequences of structural variant calls
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Jasmine
https://github.com/mkirsche/Jasmine
Package description
SV Merging Across Samples
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Kalign
https://github.com/TimoLassmann/kalign
Package description
Kalign is a fast multiple sequence alignment program for biological sequences.
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LUMPY
https://github.com/arq5x/lumpy-sv
Package description
A probabilistic framework for structural variant discovery.
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LocalColabFold
https://github.com/YoshitakaMo/localcolabfold
Package description
LocalColabFold is an installer script designed to make ColabFold functionality available on users' local machines.
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MACSE
https://bioweb.supagro.inra.fr/macse/index.php
Package description
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure.
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MAFFT
https://mafft.cbrc.jp/alignment/software/
Package description
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.
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MM-align
https://zhanggroup.org/MM-align
Package description
MM-align is an algorithm for structurally aligning a pair of multiple-chain protein complexes. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. An optimal alignment between two complexes, as well as the overall TM-score, will be reported.
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MMseqs2
Package description
MMseqs2: ultra fast and sensitive search and clustering suite
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MUSCLE
Package description
MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.
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MaxAlign
https://services.healthtech.dtu.dk/service.php?MaxAlign-1.1
Package description
In phylogenetic analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses.
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MethylDackel
https://github.com/dpryan79/MethylDackel
Package description
A (mostly) universal methylation extractor for BS-seq experiments.
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MrBayes
https://nbisweden.github.io/MrBayes/
Package description
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.
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MultiQC
Package description
Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
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NGS
Package description
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
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OpenFold
https://github.com/aqlaboratory/openfold
Package description
A faithful PyTorch reproduction of DeepMind's AlphaFold 2
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OpenMM
Package description
OpenMM is a toolkit for molecular simulation.
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PAML
http://abacus.gene.ucl.ac.uk/software/paml.html
Package description
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
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PLINK
https://www.cog-genomics.org/plink/2.0/
Package description
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
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PRANK
http://wasabiapp.org/software/prank/
Package description
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.
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PREQUAL
https://github.com/simonwhelan/prequal
Package description
A program to identify and mask regions with non-homologous adjacent characters in FASTA files.
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PSIPRED
Package description
Accurate protein secondary structure prediction
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Pindel
http://gmt.genome.wustl.edu/packages/pindel/
Package description
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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PyRosetta
Package description
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
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Pysam
https://github.com/pysam-developers/pysam
Package description
Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
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Qualimap
http://qualimap.bioinfo.cipf.es/
Package description
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
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R-bundle-Bioconductor
Package description
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
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RAxML
https://github.com/stamatak/standard-RAxML
Package description
RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
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RFdiffusion
https://github.com/RosettaCommons/RFdiffusion
Package description
RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges as we have outlined in the RFdiffusion paper.
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RSEM
https://deweylab.github.io/RSEM/
Package description
RNA-Seq by Expectation-Maximization
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Racon
https://github.com/lbcb-sci/racon
Package description
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
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RegTools
https://regtools.readthedocs.org
Package description
RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
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RoseTTAFold2NA
https://github.com/uw-ipd/RoseTTAFold2NA
Package description
RoseTTAFold2 protein/nucleic acid complex prediction
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Rosetta
https://www.rosettacommons.org
Package description
Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.
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SAMtools
Package description
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
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SRA-Toolkit
https://github.com/ncbi/sra-tools
Package description
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
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STAR
https://github.com/alexdobin/STAR
Package description
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
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SURVIVOR
https://github.com/fritzsedlazeck/SURVIVOR
Package description
Toolset for SV simulation, comparison and filtering
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SVTyper
https://github.com/hall-lab/svtyper
Package description
SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data.
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Salmon
https://github.com/COMBINE-lab/salmon
Package description
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
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Sambamba
https://lomereiter.github.io/sambamba/
Package description
Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
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Subread
https://subread.sourceforge.net/
Package description
High performance read alignment, quantification and mutation discovery
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T-COFFEE
Package description
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures.
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TranslatorX
Package description
Nucleotide sequence alignment and alignment cleaning based on amino acid information.
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Trim_Galore
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Package description
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).
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VEP
https://www.ensembl.org/info/docs/tools/vep
Package description
Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.
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bx-python
https://github.com/bxlab/bx-python
Package description
The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
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cooler
https://open2c.github.io/cooler
Package description
Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.
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cutadapt
https://opensource.scilifelab.se/projects/cutadapt/
Package description
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
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e3nn
Package description
Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant neural networks for the group O(3).
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gsort
https://github.com/brentp/gsort
Package description
gsort is a tool to sort genomic files according to a genomefile
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kallisto
https://pachterlab.github.io/kallisto/
Package description
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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lDDT
Package description
The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.
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mTM-align
http://yanglab.nankai.edu.cn/mTM-align/
Package description
mTM-align is a server for for efficient protein structure comparisons, which includes are two related modules. The first is for fast database search with one input structure. The second is for multiple structure alignment with two or more input structures. For the first module, it takes about 2-5 minutes for a structure of a medium size (~300 residues). After the search is done, a multiple structure alignment is performed automatically with the top 10 structure, using the second module. The users are also able to select other structures from the returned list to perform multiple structure alignment. For the second module, it takes a few seconds for input of ~10 structures of medium size.
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manta
https://github.com/Illumina/manta
Package description
Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
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minimap2
https://github.com/lh3/minimap2
Package description
Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.
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mosdepth
https://github.com/brentp/mosdepth
Package description
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
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ncbi-vdb
https://github.com/ncbi/ncbi-vdb
Package description
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
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parabricks
https://docs.nvidia.com/clara/parabricks/v3.6.1/text/software_overview.html#what-is-clara-parabricks
Package description
Parabricks is a software suite for performing secondary analysis of next generation sequencing (NGS) DNA and RNA data.
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picard
https://broadinstitute.github.io/picard/
Package description
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
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preseq
https://smithlabresearch.org/software/preseq
Package description
Software for predicting library complexity and genome coverage in high-throughput sequencing.
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prodigal
https://github.com/hyattpd/Prodigal/
Package description
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
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pyBigWig
https://github.com/deeptools/pyBigWig
Package description
A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.
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pyGenomeTracks
https://pygenometracks.readthedocs.io
Package description
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.
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pybedtools
https://daler.github.io/pybedtools
Package description
pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
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pyfaidx
https://pypi.python.org/pypi/pyfaidx
Package description
pyfaidx: efficient pythonic random access to fasta subsequences
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samblaster
https://github.com/GregoryFaust/samblaster
Package description
samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.
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smoove
https://github.com/brentp/smoove
Package description
smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls.
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strelka
https://github.com/Illumina/strelka
Package description
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
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svaba
https://github.com/walaj/svaba
Package description
SvABA - Structural variation and indel analysis by assembly
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svtools
https://github.com/hall-lab/svtools
Package description
svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls.
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tMAE
https://github.com/mumichae/tMAE
Package description
Package containing functions to: perform a negative binomial test on allele-specific counts add gnomAD minor allele frequencies MAplot (FC vs total counts) of allele-specific counts and results allelic counts (ALT vs REF)
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wham
Package description
duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls