Alternatives and similar repositories for java-genomics-io

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

• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• wtsi-npg / illumina2bam
  Generate and process BAM files from Illumina sequencing instrument files
  ☆23Updated 9 years ago
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 3 years ago
• AlistairNWard / vcfPytools
  vcf file manipulation
  ☆22Updated 10 years ago
• brentp / rare-disease-wf
  (WIP) best-practices workflow for rare disease
  ☆62Updated last year
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆72Updated 7 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆90Updated last year
• dnanexus / dxWDL
  Workflow Description Language compiler for the DNAnexus platform
  ☆42Updated 2 years ago
• roryk / tiny-test-data
  Super small biological datasets for unit testing
  ☆61Updated 5 years ago
• lganel / SVScore
  Prioritize structural variants based on CADD scores
  ☆29Updated 5 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 6 years ago
• ucdavis-bioinformatics / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆25Updated 10 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• molgenis / ngs-utils
  Collection of notes and scripts related to NGS
  ☆14Updated 8 months ago
• lh3 / hapdip
  The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data
  ☆31Updated 7 years ago
• griffithlab / civic-client
  Web client for CIViC: Clinical Interpretations of Variants in Cancer
  ☆50Updated last year
• brentp / irelate
  Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang
  ☆47Updated 5 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 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
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆109Updated 4 years ago
• Ensembl / ensembl-variation
  The Ensembl Variation Perl API and SQL schema
  ☆30Updated last week
• 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
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• lh3 / CHM-eval
  ☆54Updated 5 years ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• moonso / vcf_parser
  Simple vcf parser, based on PyVCF
  ☆47Updated 6 years ago