Alternatives and similar repositories for skewer

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

• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 2 months ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆102Updated 4 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆122Updated 3 months ago
• grenaud / deML
  Maximum likelihood demultiplexing
  ☆47Updated 5 months ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆105Updated 3 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆137Updated 5 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆78Updated last year
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆87Updated 9 months ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆72Updated 9 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
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 6 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆90Updated 5 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆97Updated last year
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆71Updated last month
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated 2 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• najoshi / sabre
  ☆63Updated 4 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated 2 weeks ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• MultiQC / MegaQC
  Web application to collect and visualise data across multiple MultiQC runs.
  ☆97Updated 7 months ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆101Updated 2 years ago
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆63Updated 7 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆72Updated 3 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆98Updated 3 years ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆137Updated last month
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• parklab / bamsnap
  ☆123Updated this week