Alternatives and similar repositories for PyVCF

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

• schatzlab / appliedgenomics2017
  JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
  ☆58Updated 7 years ago
• Clinical-Genomics / chanjo
  Chanjo provides a better way to analyze coverage data in clinical sequencing.
  ☆51Updated 10 months ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆89Updated 6 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• mgymrek / pybamview
  Browser based application for viewing bam alignments
  ☆56Updated 8 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• lh3 / CHM-eval
  ☆54Updated 5 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆91Updated last year
• sequencing / gvcftools
  Utilities to create and analyze gVCF files
  ☆38Updated 8 years ago
• DaehwanKimLab / hisat
  Fast spliced aligner with low memory requirements
  ☆41Updated 10 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 3 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆84Updated last month
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆84Updated 4 years ago
• Illumina / canvas
  Canvas - Copy number variant (CNV) calling from DNA sequencing data
  ☆128Updated 6 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• arq5x / cyvcf
  A fast Python library for VCF files leveraging Cython for speed.
  ☆52Updated 7 years ago
• fls-bioinformatics-core / genomics
  Scripts, utilities and programs for genomic bioinformatics.
  ☆83Updated last month
• 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
• relipmoc / skewer
  ☆95Updated 3 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• umd-byob / presentations
  Bring Your Own Bioinformatics
  ☆27Updated 9 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆54Updated 8 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆122Updated 5 months ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago