Alternatives and similar repositories for bioawk

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

• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆834Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆450Updated 3 weeks ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆723Updated last week
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆985Updated 4 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆504Updated last month
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆475Updated 2 weeks ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆513Updated 4 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆503Updated 8 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆515Updated last week
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆421Updated 10 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆422Updated 6 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆344Updated 2 months ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆495Updated this week
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆305Updated last month
• cole-trapnell-lab / cufflinks
  ☆317Updated 5 years ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆683Updated this week
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆593Updated 6 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆748Updated 3 months ago
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆621Updated 2 years ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆294Updated 9 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆602Updated 11 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,476Updated last month
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆693Updated 3 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated last week
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆375Updated 3 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆766Updated 2 weeks ago