Read trimming tool for Illumina NGS data.
☆152Mar 10, 2015Updated 11 years ago
Alternatives and similar repositories for trimmomatic
Users that are interested in trimmomatic are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Cutadapt removes adapter sequences from sequencing reads☆576Apr 6, 2026Updated last week
- A fast and sensitive gapped read aligner☆787Mar 7, 2026Updated last month
- A quality control analysis tool for high throughput sequencing data☆594Mar 20, 2026Updated 3 weeks ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,730Mar 22, 2025Updated last year
- ☆301Mar 10, 2026Updated last month
- 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.
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,324Apr 8, 2026Updated last week
- A single molecule sequence assembler for genomes large and small.☆700Feb 24, 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.☆1,062Mar 24, 2026Updated 3 weeks ago
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,877Apr 11, 2026Updated last week
- Rapid prokaryotic genome annotation☆973Jan 6, 2026Updated 3 months ago
- Processing and analysis of data coming from Illumina sequencing machines☆10Updated this week
- Ultra-fast de novo assembler using long noisy reads☆136Feb 24, 2021Updated 5 years ago
- Trinity RNA-Seq de novo transcriptome assembly☆888Feb 7, 2025Updated last year
- AI Agents on 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.
- Near-optimal RNA-Seq quantification☆756Mar 16, 2026Updated last month
- TransDecoder source☆304Mar 22, 2026Updated 3 weeks ago
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆269Mar 15, 2026Updated last month
- RNA-seq aligner☆2,178Mar 18, 2025Updated last year
- Toolkit for processing sequences in FASTA/Q formats☆1,535Jun 1, 2025Updated 10 months ago
- Tools for working with SAM/BAM data☆609Dec 22, 2024Updated last year
- Pilon is an automated genome assembly improvement and variant detection tool☆381Apr 10, 2022Updated 4 years ago
- SPAdes Genome Assembler☆929Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Official code repository for GATK versions 4 and up☆1,937Updated this week
- Divide and Conquer BLAST: using grid engines to accelerate NCBI-BLAST+ and other sequence analysis tools☆11Apr 26, 2020Updated 5 years ago
- SRA Tools☆1,327Updated this week
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆727Updated this week
- ☆132Jul 9, 2023Updated 2 years ago
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆865Feb 8, 2026Updated 2 months ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆26Dec 11, 2017Updated 8 years ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆470Apr 7, 2026Updated last week
- Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"☆11Jun 8, 2018Updated 7 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆354Jul 19, 2025Updated 9 months ago
- Windowed Adaptive Trimming for fastq files using quality☆228May 8, 2017Updated 8 years ago
- Long Approximate Matches-based Split Aligner☆13Apr 6, 2017Updated 9 years ago
- Gordon's Text utils Library☆10Apr 11, 2022Updated 4 years ago
- This is *NOT* the official repository of samtools.☆49Jun 9, 2017Updated 8 years ago
- BLAST-Like Alignment Tool☆23Jan 11, 2019Updated 7 years ago
- Somatic point mutation caller☆17Jul 8, 2016Updated 9 years ago