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.
  ☆849Updated 5 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,004Updated 7 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆510Updated 2 weeks ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆470Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• marbl / Krona
  Interactively explore metagenomes and more from a web browser.
  ☆490Updated 3 years ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆509Updated 2 weeks ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆514Updated last month
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• vcftools / vcftools
  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  ☆538Updated 5 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆527Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆490Updated 2 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆694Updated last month
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆443Updated 10 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆706Updated 6 months ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆306Updated 5 months ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆427Updated last month
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆875Updated 8 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆546Updated last month
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆535Updated last month
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆595Updated 10 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• cole-trapnell-lab / cufflinks
  ☆319Updated 5 years ago
• nextflow-io / patterns
  A curated collection of Nextflow implementation patterns
  ☆365Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,503Updated 5 months ago
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆689Updated last month
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆878Updated 5 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆758Updated last week