Repositories list

• IsoQuant

  Public
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

  bioinformaticsrna-seqnanopore+ 3

  bioinformaticsrna-seqnanoporengspacbiotranscriptomics

  Python

  •

  Other

  •2222 forks•217217 stars•4545 issues•44 pull requests•Updated Apr 17, 2026Apr 17, 2026

• spades

  Public
  SPAdes Genome Assembler

  sequencingnext-generation-sequencingillumina+ 4

  sequencingnext-generation-sequencingilluminagenome-assemblysequence-assemblertranscriptome-assemblymetagenome-assembly

  C++

  •

  Other

  •159159 forks•930930 stars•290290 issues•55 pull requests•Updated Apr 13, 2026Apr 13, 2026

• viralVerify

  Public
  viralVerify: viral contig verification tool

  Python

  •

  MIT License

  •1313 forks•7474 stars•55 issues•00 pull requests•Updated Feb 19, 2026Feb 19, 2026

• rnaquast

  Public
  Quality assessment of de novo transcriptome assemblies from RNA-Seq data

  transcriptome-assemblyquality-evaluation

  transcriptome-assemblyquality-evaluation

  Python

  •

  Other

  •66 forks•2727 stars•88 issues•00 pull requests•Updated Nov 14, 2025Nov 14, 2025

• nerpa

  Public
  C++

  •

  Other

  •44 forks•1818 stars•00 issues•33 pull requests•Updated Mar 20, 2025Mar 20, 2025

• quast-website

  Public
  Django web interface for Quast assembly assessment tool: https://github.com/ablab/quast

  HTML

  •22 forks•66 stars•00 issues•00 pull requests•Updated Nov 14, 2024Nov 14, 2024

• quast

  Public
  Genome assembly evaluation tool

  visualizationbioinformaticsgenome-assembly-evaluation+ 1

  visualizationbioinformaticsgenome-assembly-evaluationcontigs

  AMPL

  •

  Other

  •8888 forks•509509 stars•8383 issues•44 pull requests•Updated Nov 14, 2024Nov 14, 2024

• metarna

  Public
  Python

  •00 forks•00 stars•00 issues•22 pull requests•Updated Jul 6, 2023Jul 6, 2023

• orf-search

  Public
  ORF search on assembly graphs

  Python

  •

  Other

  •33 forks•66 stars•00 issues•00 pull requests•Updated Apr 12, 2023Apr 12, 2023

• metaGT

  Public

  ablab/metaGT’s past year of commit activity
  Pipeline for metagenome and metatranscriptome joint assembly

  metagenomicsmetatranscriptomics

  metagenomicsmetatranscriptomics

  Nextflow

  •

  MIT License

  •33 forks•2020 stars•33 issues•00 pull requests•Updated Mar 3, 2023Mar 3, 2023

• VerityMap

  Public
  C++

  •

  GNU General Public License v3.0

  •55 forks•3939 stars•1010 issues•11 pull request•Updated Feb 22, 2023Feb 22, 2023

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2023Jan 22, 2023

• graphamr

  Public
  Antibiotic prediction from metagenome assembly graphs

  Nextflow

  •22 forks•88 stars•33 issues•11 pull request•Updated Sep 19, 2022Sep 19, 2022

• stringdecomposer

  Public
  Tool for decomposition centromeric assemblies and long reads into monomers

  C++

  •

  Other

  •22 forks•3737 stars•55 issues•00 pull requests•Updated Sep 17, 2022Sep 17, 2022

• npdtools

  Public
  Natural Product Discovery tools -- a toolkit containing various pipelines for in silico analysis of natural product mass spectrometry data

  bioinformaticsmetabolomicsmass-spectrometry+ 1

  bioinformaticsmetabolomicsmass-spectrometrynatural-products

  99 forks•2929 stars•44 issues•00 pull requests•Updated Aug 19, 2022Aug 19, 2022

• quast_snakemake

  Public
  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 29, 2022Jul 29, 2022

• NPvis

  Public
  Interactive visualizer for MS/MS fragmentation of natural products

  JavaScript

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jun 21, 2022Jun 21, 2022

• HORmon

  Public
  Python

  •

  Other

  •11 fork•88 stars•11 issue•11 pull request•Updated May 6, 2022May 6, 2022

• platform_comparison

  Public
  Comparing Platforms

  Python

  •

  Other

  •11 fork•22 stars•00 issues•00 pull requests•Updated Feb 2, 2022Feb 2, 2022

• holy-build-box

  Public
  System for building cross-distribution Linux binaries

  Shell

  •

  MIT License

  •7676 forks•00 stars•00 issues•00 pull requests•Updated Jan 31, 2022Jan 31, 2022

• viralComplete

  Public
  viralComplete: BLAST-based viral completeness verification

  Python

  •11 fork•2323 stars•00 issues•00 pull requests•Updated Oct 4, 2021Oct 4, 2021

• TandemTools

  Public
  Tool for assessing/improving assembly quality in extra-long tandem repeats

  C++

  •

  Other

  •55 forks•4848 stars•1010 issues•11 pull request•Updated Feb 23, 2021Feb 23, 2021

• covid19_variation_analysis

  Public
  Python

  •22 forks•11 star•00 issues•00 pull requests•Updated Jun 21, 2020Jun 21, 2020

• plasmidVerify

  Public
  plasmidVerify: plasmid contig verification tool

  Python

  •33 forks•1515 stars•22 issues•00 pull requests•Updated Apr 30, 2020Apr 30, 2020

• y-tools

  Public
  C++

  •

  Other

  •22 forks•33 stars•00 issues•11 pull request•Updated Jul 26, 2018Jul 26, 2018

• basespace_gatk_app

  Public
  Repo for creating BaseSpace Apps

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 27, 2015Dec 27, 2015

• rectangles

  Public archive
  Python

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 20, 2012Dec 20, 2012

• external-tools

  Public archive
  C++

  •00 forks•44 stars•00 issues•00 pull requests•Updated Mar 15, 2012Mar 15, 2012

• TagFinder05

  Public archive
  Java

  •11 fork•33 stars•00 issues•00 pull requests•Updated Mar 6, 2012Mar 6, 2012

• TagFinder

  Public archive
  Java

  •11 fork•44 stars•00 issues•00 pull requests•Updated Mar 6, 2012Mar 6, 2012