Alternatives and similar repositories for repaq

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

• imgag / ngs-bits
  Short-read and long-read sequencing tools for diagnostics
  ☆172Updated last week
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆139Updated 4 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆173Updated last year
• OpenGene / gencore
  Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
  ☆126Updated 2 years ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated 2 weeks ago
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆237Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆250Updated 3 months ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆130Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 3 months ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆152Updated 2 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆197Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆201Updated 4 months ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆118Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆275Updated 2 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆252Updated 5 months ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆188Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• BGI-flexlab / SOAPnuke
  A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files
  ☆112Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆230Updated 3 years ago
• OpenGene / fastv
  An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infect…
  ☆118Updated 2 years ago
• mozack / abra2
  ABRA2
  ☆95Updated 3 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆118Updated 6 years ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• shiquan / bamdst
  a lightweight bam file depth statistical tool
  ☆158Updated last year
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆203Updated 4 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 3 months ago