Cutadapt removes adapter sequences from sequencing reads
☆575Apr 6, 2026Updated this 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:
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆544Feb 24, 2026Updated last month
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- A quality control analysis tool for high throughput sequencing data☆591Mar 20, 2026Updated 3 weeks ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,437Mar 28, 2026Updated 2 weeks ago
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,319Mar 30, 2026Updated last week
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A fast and sensitive gapped read aligner☆785Mar 7, 2026Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,726Mar 22, 2025Updated last year
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,873Mar 26, 2026Updated 2 weeks ago
- Efficiently read and write sequencing data from Python☆70Oct 12, 2025Updated 5 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,534Jun 1, 2025Updated 10 months ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆543Mar 2, 2026Updated last month
- A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.☆1,056Mar 24, 2026Updated 2 weeks ago
- C++ API & command-line toolkit for working with BAM data☆429May 18, 2025Updated 10 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆470Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- RNA-seq aligner☆2,174Mar 18, 2025Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆530Jan 27, 2026Updated 2 months ago
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆876Mar 11, 2026Updated last month
- Next generation sequencing reads de novo assembler.☆239Sep 20, 2025Updated 6 months ago
- C library for high-throughput sequencing data formats☆913Apr 2, 2026Updated last week
- Tools to process and analyze deep sequencing data.☆753Jul 23, 2025Updated 8 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,153Feb 13, 2026Updated last month
- Transcript assembly and quantification for RNA-Seq☆498Dec 26, 2025Updated 3 months ago
- Read trimming tool for Illumina NGS data.☆152Mar 10, 2015Updated 11 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,536Mar 31, 2026Updated last week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆864Feb 8, 2026Updated 2 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆214May 14, 2020Updated 5 years ago
- Windowed Adaptive Trimming for fastq files using quality☆228May 8, 2017Updated 8 years ago
- SRA Tools☆1,326Updated this week
- Tools for working with SAM/BAM data☆609Dec 22, 2024Updated last year
- An NGS read trimming tool that is specific, sensitive, and speedy. (production)☆126Mar 22, 2026Updated 2 weeks ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆468Mar 15, 2026Updated 3 weeks ago
- Near-optimal RNA-Seq quantification☆755Mar 16, 2026Updated 3 weeks ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- The next version of bwa-mem☆826Oct 15, 2025Updated 5 months ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆702Oct 28, 2025Updated 5 months ago
- FASTA/FASTQ pre-processing programs☆199Mar 4, 2022Updated 4 years ago
- BWK awk modified for biological data☆639Aug 11, 2022Updated 3 years ago
- Versatile open-source tool for microbiome analysis☆742Updated this week
- A single molecule sequence assembler for genomes large and small.☆699Feb 24, 2026Updated last month
- Accelerated BLAST compatible local sequence aligner.☆1,278Mar 28, 2026Updated last week