Alternatives and similar repositories for cutadapt

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

• jts / nanopolish
  Signal-level algorithms for MinION data
  ☆589Updated 2 years ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆519Updated 4 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆427Updated 3 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆455Updated 2 weeks ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆426Updated 7 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆447Updated last year
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆857Updated 3 months ago
• usadellab / Trimmomatic
  ☆259Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆296Updated 10 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆640Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆507Updated 8 months ago
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆534Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆367Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆466Updated last week
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆419Updated 6 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆603Updated last year
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆520Updated last year
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆490Updated last week
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆468Updated 2 months ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆493Updated 2 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆236Updated 4 years ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆771Updated last month
• ablab / quast
  Genome assembly evaluation tool
  ☆451Updated 8 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆519Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆478Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆726Updated 2 weeks ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆606Updated 3 weeks ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆518Updated last week
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆663Updated 4 months ago