Alternatives and similar repositories for bcbio-nextgen

Users that are interested in bcbio-nextgen are comparing it to the libraries listed below

• chapmanb / bcbb
  Incubator for useful bioinformatics code, primarily in Python and R
  ☆632Updated 8 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,004Updated 7 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,372Updated this week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆845Updated 4 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆703Updated 6 months ago
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆858Updated last month
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,503Updated 4 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated last week
• igvteam / igv
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
  ☆699Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆692Updated last month
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆508Updated last week
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆875Updated 8 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆841Updated last year
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆546Updated 3 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,118Updated last week
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆845Updated last year
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆514Updated last month
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• nextflow-io / awesome-nextflow
  A curated list of nextflow based pipelines
  ☆607Updated 4 months ago
• BioContainers / containers
  Bioinformatics containers
  ☆757Updated last month
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆511Updated last week
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆526Updated 3 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,050Updated 3 years ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆447Updated last year
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,040Updated 3 months ago
• lh3 / bioawk
  BWK awk modified for biological data
  ☆630Updated 3 years ago
• ncbi / sra-tools
  SRA Tools
  ☆1,262Updated last week
• igvteam / igv.js
  Embeddable genomic visualization component based on the Integrative Genomics Viewer
  ☆690Updated this week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆830Updated last year