Cutadapt removes adapter sequences from sequencing reads
☆582Jun 22, 2026Updated last week
Alternatives and similar repositories for cutadapt
Users that are interested in cutadapt are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆561Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,040Jun 10, 2026Updated 2 weeks ago
- A quality control analysis tool for high throughput sequencing data☆602Jun 22, 2026Updated last week
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,465Jun 20, 2026Updated last week
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,384Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A fast and sensitive gapped read aligner☆795Jun 1, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,752Jun 20, 2026Updated last week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,917Jun 18, 2026Updated last week
- Efficiently read and write sequencing data from Python☆70Oct 12, 2025Updated 8 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,542Jun 1, 2025Updated last year
- Tools for handling Unique Molecular Identifiers in NGS data sets☆549Jun 18, 2026Updated last week
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,067Jun 13, 2026Updated 2 weeks ago
- C++ API & command-line toolkit for working with BAM data☆430May 18, 2025Updated last year
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆472Apr 21, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- RNA-seq aligner☆2,216Mar 18, 2025Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆539Jan 27, 2026Updated 5 months ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆898Jun 23, 2026Updated last week
- Next generation sequencing reads de novo assembler.☆240Sep 20, 2025Updated 9 months ago
- C library for high-throughput sequencing data formats☆931Updated this week
- Tools to process and analyze deep sequencing data.☆762Jun 24, 2026Updated last week
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,204May 19, 2026Updated last month
- Read trimming tool for Illumina NGS data.☆152Mar 10, 2015Updated 11 years ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,573Jun 24, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Transcript assembly and quantification for RNA-Seq☆516Jun 3, 2026Updated 3 weeks ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆871Apr 20, 2026Updated 2 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆214May 14, 2020Updated 6 years ago
- Windowed Adaptive Trimming for fastq files using quality☆229May 8, 2017Updated 9 years ago
- SRA Tools☆1,346Updated this week
- Tools for working with SAM/BAM data☆611Dec 22, 2024Updated last year
- An NGS read trimming tool that is specific, sensitive, and speedy. (production)☆126May 4, 2026Updated last month
- Near-optimal RNA-Seq quantification☆766Mar 16, 2026Updated 3 months ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆488Apr 10, 2026Updated 2 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- The next version of bwa-mem☆844Oct 15, 2025Updated 8 months ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆719Oct 28, 2025Updated 8 months ago
- FASTA/FASTQ pre-processing programs☆202Mar 4, 2022Updated 4 years ago
- BWK awk modified for biological data☆641Aug 11, 2022Updated 3 years ago
- Versatile open-source tool for microbiome analysis☆749Jun 24, 2026Updated last week
- A single molecule sequence assembler for genomes large and small.☆701Jun 18, 2026Updated last week
- Accelerated BLAST compatible local sequence aligner.☆1,307Jun 18, 2026Updated last week