multiqc

dep: [python3-click]

Command-Line Interface Creation Kit - Python 3.x

dep: [python3-coloredlogs]

colored terminal output for Python 3's logging module

dep: [python3-humanize]

Python Humanize library (Python 3)

dep: [python3-importlib-metadata]

library to access the metadata for a Python package - Python 3.x

dep: [python3-jinja2]

small but fast and easy to use stand-alone template engine

dep: [python3-markdown]

text-to-HTML conversion library/tool (Python 3 version)

dep: [python3-matplotlib]

Python based plotting system in a style similar to Matlab

dep: [python3-numpy]

Python library for numerical computations (Python 3)

dep: [python3-packaging]

core utilities for python3 packages

dep: [python3-pil]

Python Imaging Library (Python3)

dep: [python3-plotly]

Python 3 plotting library for publication-quality graphs

dep: [python3-pyaml-env]

Python3 YAML configuration with environment variables parsing

dep: [python3-requests]

elegant and simple HTTP library for Python3, built for human beings

dep: [python3-rich]

render rich text, tables, progress bars, syntax highlighting, markdown and more

dep: [python3-rich-click]

creating beautiful command line interfaces for Python3

dep: [python3-spectra]

Easy color scales and color conversion for Python (Python 3 version)

dep: [python3-yaml]

YAML parser and emitter for Python3

dep: [python3] [any]

interactive high-level object-oriented language (default python3 version)

dep: [python3-lzstring]

LZ-based compression algorithm for Python (Python 3 version)

dep: [python3-humanfriendly]

Python3 library to make user friendly text interfaces

dep: [fonts-glyphicons-halflings]

icons made for smaller graphic

dep: [libjs-bootstrap]

HTML, CSS and JS framework

dep: [libjs-jquery]

JavaScript library for dynamic web applications

dep: [libjs-jquery-tablesorter]

jQuery flexible client-side table sorting plugin

dep: [libjs-jquery-ui]

JavaScript UI library for dynamic web applications

rec: [node-clipboard]

Node.js module to copy to clipboard without flash

rec: [libjs-filesaver]

Client-side, HTML5 library for saving local files

rec: [pandoc]

general markup converter

rec: [texlive-xetex]

TeX Live: XeTeX and packages

enh: [adapterremoval]

rapid adapter trimming, identification, and read merging of gene sequences

enh: afterqc

Package not available

enh: [bamtools]

toolkit for manipulating BAM (genome alignment) files

enh: [bbmap]

BBTools genomic aligner and other tools for short sequences

enh: [bcftools]

genomic variant calling and manipulation of VCF/BCF files

enh: bcl2fastq

Package not available

enh: [biobambam2]

tools for early stage alignment file processing

enh: biobloomtools

Package not available

enh: biscuit

Package not available

enh: bismark

Package not available

enh: [bowtie]

Ultrafast memory-efficient short read aligner

enh: [bowtie2]

ultrafast memory-efficient short read aligner

enh: [busco]

benchmarking sets of universal single-copy orthologs

enh: clipandmerge

Package not available

enh: clusterflow

Package not available

enh: conpair

Package not available

enh: [cutadapt]

Clean biological sequences from high-throughput sequencing reads

enh: damageprofiler

Package not available

enh: dedup

Package not available

enh: deeptools

Package not available

enh: disambiguate

Package not available

enh: dragen

Package not available

enh: [fastp]

Ultra-fast all-in-one FASTQ preprocessor

enh: fastq-screen

Package not available

enh: [fastqc]

quality control for high throughput sequence data

enh: featurecounts

Package not available

enh: fgbio

Package not available

enh: [flash]

Fast Length Adjustment of SHort reads

enh: [flexbar]

flexible barcode and adapter removal for sequencing platforms

enh: gatk

Package not available

enh: goleft-indexcov

Package not available

enh: [happy]

Parser generator for Haskell

enh: hicexplorer

Package not available

enh: hicpro

Package not available

enh: hicup

Package not available

enh: [hisat2]

graph-based alignment of short nucleotide reads to many genomes

enh: homer

Package not available

enh: htseq

Package not available

enh: interop

Package not available

enh: [ivar]

functions broadly useful for viral amplicon-based sequencing

enh: [jellyfish]

count k-mers in DNA sequences

enh: kaiju

Package not available

enh: [kallisto]

near-optimal RNA-Seq quantification

enh: kat

Package not available

enh: [kraken]

assigning taxonomic labels to short DNA sequences

enh: leehom

Package not available

enh: longranger

Package not available

enh: macs2

Package not available

enh: [malt]

sequence alignment and analysis tool to process sequencing data

enh: methylqa

Package not available

enh: minionqc

Package not available

enh: [mirtop]

annotate miRNAs with a standard mirna/isomir naming

enh: mirtrace

Package not available

enh: mosdepth

Package not available

enh: mtnucratio

Package not available

enh: multivcfanalyzer

Package not available

enh: peddy

Package not available

enh: phantompeakqualtools

Package not available

enh: [picard-tools]

Command line tools to manipulate SAM and BAM files

enh: preseq

Package not available

enh: [prokka]

rapid annotation of prokaryotic genomes

enh: [pycoqc]

computes metrics and generates Interactive QC plots

enh: qorts

Package not available

enh: qualimap

Package not available

enh: quast

Package not available

enh: rna-seqc

Package not available

enh: [rna-star]

ultrafast universal RNA-seq aligner

enh: [rockhopper]

system for analyzing bacterial RNA-seq data

enh: [rsem]

RNA-Seq by Expectation-Maximization

enh: rseqc

Package not available

enh: [salmon]

wicked-fast transcript quantification from RNA-seq data

enh: [samblaster]

marks duplicates, extracts discordant/split reads

enh: [samtools]

processing sequence alignments in SAM, BAM and CRAM formats

enh: sargasso

Package not available

enh: seqyclean

Package not available

enh: sexdeterrmine

Package not available

enh: [sickle]

windowed adaptive trimming tool for FASTQ files using quality

enh: [skewer]

post-processing of high-throughput DNA sequence reads

enh: slamdunk

Package not available

enh: [snpeff]

genetic variant annotation and effect prediction toolbox - tool

enh: snpsplit

Package not available

enh: somalier

Package not available

enh: [sortmerna]

tool for filtering, mapping and OTU-picking NGS reads

enh: [stacks]

pipeline for building loci from short-read DNA sequences

enh: supernova

Package not available

enh: theta2

Package not available

enh: [trimmomatic]

flexible read trimming tool for Illumina NGS data

enh: varscan2

Package not available

enh: [vcftools]

Collection of tools to work with VCF files

enh: verifybamid

Package not available