Cutadapt removes adapter sequences from sequencing reads
☆586Jul 27, 2026Updated 2 weeks ago
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☆569Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,045Jun 10, 2026Updated 2 months ago
- A quality control analysis tool for high throughput sequencing data☆613Jul 20, 2026Updated 3 weeks ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,484Aug 2, 2026Updated last week
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,410Jul 30, 2026Updated last week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A fast and sensitive gapped read aligner☆809Jun 1, 2026Updated 2 months ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,765Updated this week
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,939Updated this week
- Efficiently read and write sequencing data from Python☆70Oct 12, 2025Updated 9 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,553Jun 1, 2025Updated last year
- Tools for handling Unique Molecular Identifiers in NGS data sets☆549Jun 18, 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.☆1,070Jul 31, 2026Updated last week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆475Updated this week
- C++ API & command-line toolkit for working with BAM data☆431May 18, 2025Updated last year
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- RNA-seq aligner☆2,230Mar 18, 2025Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆539Jul 31, 2026Updated last week
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆925Updated this week
- Next generation sequencing reads de novo assembler.☆242Sep 20, 2025Updated 10 months ago
- C library for high-throughput sequencing data formats☆940Updated this week
- Tools to process and analyze deep sequencing data.☆762Updated this week
- Read trimming tool for Illumina NGS data.☆152Mar 10, 2015Updated 11 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,230May 19, 2026Updated 2 months ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,589Jul 8, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Transcript assembly and quantification for RNA-Seq☆527Updated this week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆876Apr 20, 2026Updated 3 months ago
- SRA Tools☆1,361Updated this week
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆213May 14, 2020Updated 6 years ago
- An NGS read trimming tool that is specific, sensitive, and speedy. (production)☆126May 4, 2026Updated 3 months ago
- Windowed Adaptive Trimming for fastq files using quality☆229May 8, 2017Updated 9 years ago
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆493Jul 7, 2026Updated last month
- Near-optimal RNA-Seq quantification☆769Jul 12, 2026Updated 3 weeks ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- The next version of bwa-mem☆858Oct 15, 2025Updated 9 months ago
- Ultra-fast and memory-efficient (meta-)genome assembler☆721Oct 28, 2025Updated 9 months ago
- FASTA/FASTQ pre-processing programs☆202Mar 4, 2022Updated 4 years ago
- BWK awk modified for biological data☆643Aug 11, 2022Updated 4 years ago
- Versatile open-source tool for microbiome analysis☆754Updated this week
- A single molecule sequence assembler for genomes large and small.☆707Jun 18, 2026Updated last month
- Accelerated BLAST compatible local sequence aligner.☆1,313Updated this week