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bowtie2

breakdancer

SV detection from paired end reads mapping

breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R. More information at

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

clineff

cortex

reference free variant assembly

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

fastqc

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

htslib

C library for high-throughput sequencing data formats

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

mace

neat-genreads

NEAT read simulation tools

pear

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

pindel

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.

prinseq

prinseq-lite-0.20.4

root

The official repository for ROOT: analyzing, storing and visualizing big data, scientifically

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scythe

A 3'-end adapter contaminant trimmer

sickle

Windowed Adaptive Trimming for fastq files using quality

simug

simuG: a general-purpose genome simulator

slurm

slurm repository. Originally from https://github.com/SchedMD/slurm

snpeff

speedseq

A flexible framework for rapid genome analysis and interpretation

stampy

tectonic

varcap

Variant Calling and Postfiltering

varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data

vcftools

0.1.13