R

Free software environment for statistical computing and graphics

apptainer

Application containers for linux (previously known as Singularity)

apptainer

bedops

Suite of tools for addressing questions arising in genomics studies

bedtools

Powerful toolset for genome arithmetic

fastp

Ultra-fast all-in-one FASTQ preprocessor

genmap

Ultra-fast computation of genome mappability

hisat2

Graph based aligner

isa-l

Collection of optimised low-level functions targeting storage applications

last

Genomic sequence aligner

minia

Short read genome assembler

mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

octopus

Bayesian haplotype-based mutation calling

picard-tools

Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF

python3.12-bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

python3.12-cnvkit

Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data

python3.12-pyfaidx

Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index

python3.12-python-lzo

Python bindings for the LZO data compression library

bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

cnvkit

Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data