Alternatives and similar repositories for repaq

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

• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆128Updated 3 years ago
• OpenGene / gencore
  Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
  ☆123Updated last year
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated last month
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• shubhamchandak94 / Spring
  FASTQ compression
  ☆131Updated 2 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated last week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆167Updated last year
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆247Updated this week
• brentp / echtvar
  using all the bits for echt rapid variant annotation and filtering
  ☆153Updated 5 months ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆116Updated 8 months ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆74Updated 6 years ago
• BGI-flexlab / SOAPnuke
  A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files
  ☆109Updated last year
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆235Updated 4 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆226Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆87Updated last month
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆239Updated last month
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆135Updated 2 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆184Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆200Updated 4 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated 3 weeks ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆138Updated this week
• imgag / ngs-bits
  Short-read and long-read sequencing tools for diagnostics
  ☆165Updated this week