Alternatives and similar repositories for bcbio-nextgen-vm

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

• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆88Updated 5 years ago
• percyfal / snakemakelib
  Snakemake library for bioinformatics programs, with a focus on next-generation sequencing
  ☆22Updated 9 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆84Updated 7 years ago
• arq5x / cyvcf
  A fast Python library for VCF files leveraging Cython for speed.
  ☆52Updated 7 years ago
• sequencing / isaac_variant_caller
  This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka
  ☆37Updated 8 years ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆85Updated 3 years ago
• Clinical-Genomics / chanjo
  Chanjo provides a better way to analyze coverage data in clinical sequencing.
  ☆50Updated 5 months ago
• sjackman / docker-bio
  Docker images of bioinformatics software
  ☆21Updated 7 years ago
• h3abionet / h3agatk
  ☆21Updated 4 years ago
• enasequence / cramtools
  CRAM format specification and java API for read data.
  ☆60Updated 6 years ago
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• dnanexus-archive / samtools
  ☆30Updated 8 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 5 years ago
• chapmanb / bcbio.variation
  Toolkit to analyze genomic variation data, built on the GATK with Clojure
  ☆66Updated 9 years ago
• BauerLab / ngsane
  Analysis Framework for Biological Data from High Throughput Experiments
  ☆34Updated 8 years ago
• ewels / clusterflow
  A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
  ☆97Updated 2 years ago
• bcbio / bcbio.variation.recall
  Parallel merging, squaring off and ensemble calling for genomic variants
  ☆20Updated 5 years ago
• HAShihab / fathmm-MKL
  Predict the functional consequences of both coding and non-coding single nucleotide variants (SNVs)
  ☆20Updated 4 years ago
• fls-bioinformatics-core / genomics
  Scripts, utilities and programs for genomic bioinformatics.
  ☆83Updated 2 weeks ago
• liyao001 / BioQueue
  A novel pipeline framework to accelerate bioinformatics analysis
  ☆29Updated 2 years ago
• genome / gms
  The Genome Modeling System installer
  ☆78Updated 9 years ago
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆79Updated last month
• pachterlab / kallisto_paper_analysis
  Analysis from kallisto paper
  ☆32Updated 9 years ago
• bioboxes / rfc
  Request for comments on interchangeable bioinformatics containers
  ☆40Updated 5 years ago
• daler / metaseq
  Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
  ☆87Updated 4 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• pcingola / SnpSift
  ☆38Updated 3 months ago
• broadinstitute / gatk-protected
  Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
  ☆32Updated 7 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago