Alternatives and similar repositories for genomics

Users that are interested in genomics are comparing it to the libraries listed below

• frankMusacchia / Annocript
  Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved …
  ☆55Updated 5 years ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated 2 years ago
• lpantano / seqcluster
  small RNA analysis from NGS data
  ☆37Updated 11 months ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆63Updated 7 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• trinityrnaseq / RNASeq_Trinity_Tuxedo_Workshop
  materials for the RNA-Seq workshop on Trinity and Tuxedo, covering de novo and genome-guided transcript assembly and downstream analysis.
  ☆47Updated 8 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 2 years ago
• NCBI-Hackathons / Community_Software_Tools_for_NGS
  ☆62Updated 8 years ago
• lpryszcz / bin
  My bioinfo toolbox
  ☆50Updated 6 months ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆72Updated 9 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆47Updated 9 years ago
• relipmoc / skewer
  ☆95Updated 2 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆72Updated 3 years ago
• peterjc / picobio
  Miscellaneous Bioinformatics scripts etc mostly in Python
  ☆45Updated this week
• friend1ws / EBCall
  an empirical Bayesian framework for mutation detection from cancer genome sequencing data
  ☆31Updated 9 years ago
• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆56Updated 8 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• tfwillems / HipSTR
  Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
  ☆98Updated 2 years ago
• tseemann / VelvetOptimiser
  Automatically optimise three of Velvet's assembly parameters.
  ☆47Updated 2 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆144Updated 8 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆122Updated 3 months ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆86Updated 10 months ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆88Updated 6 years ago