Alternatives and similar repositories for seqtk:

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

• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆845Updated 5 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,257Updated this week
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆672Updated last month
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆731Updated 5 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆952Updated 2 weeks ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆718Updated 2 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆970Updated this week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆692Updated this week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆491Updated 2 months ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆1,993Updated 2 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆735Updated 3 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…
  ☆484Updated this week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆754Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆690Updated last month
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆511Updated 3 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆973Updated 3 years ago
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆763Updated 5 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆667Updated this week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆587Updated 8 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆803Updated 5 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆403Updated 3 weeks ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆402Updated 3 weeks ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆786Updated 8 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆792Updated this week
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆789Updated 6 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆469Updated last year
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆462Updated 4 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆491Updated this week
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆577Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆801Updated 7 months ago