Alternatives and similar repositories for bcbio.variation:

Users that are interested in bcbio.variation are comparing it to the libraries listed below

• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆55Updated 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.
  ☆48Updated 5 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• arq5x / bedtools-protocols
  ☆78Updated 11 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…
  ☆65Updated 2 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆73Updated 6 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• pcingola / SnpSift
  ☆38Updated last month
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆79Updated this week
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆88Updated 5 years ago
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 2 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆82Updated 6 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆82Updated 5 months ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆62Updated 7 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆97Updated 2 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆80Updated 5 months ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆34Updated 8 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆52Updated 7 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 7 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆72Updated 5 years ago
• tjparnell / biotoolbox
  Tools for querying and analysis of genomic data
  ☆27Updated 3 months ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆76Updated last year
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 9 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆96Updated 5 years ago
• fls-bioinformatics-core / genomics
  Scripts, utilities and programs for genomic bioinformatics.
  ☆82Updated last month
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 5 years ago