Alternatives and similar repositories for skewer

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

• grenaud / deML
  Maximum likelihood demultiplexing
  ☆48Updated 9 months ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆125Updated 6 months ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆68Updated 4 years ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆74Updated 4 months ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated last week
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 5 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆98Updated last year
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 2 months ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆76Updated 3 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆108Updated last month
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆107Updated 4 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆103Updated 3 years ago
• lh3 / tabtk
  Toolkit for processing TAB-delimited format
  ☆62Updated last year
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆151Updated 3 weeks ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆89Updated last year
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 6 months ago
• najoshi / sabre
  ☆63Updated 4 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 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
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆72Updated 7 years ago