SRA Tools
☆1,355Jul 21, 2026Updated this week
Alternatives and similar repositories for sra-tools
Users that are interested in sra-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,400Jul 10, 2026Updated 2 weeks ago
- RNA-seq aligner☆2,226Mar 18, 2025Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,220May 19, 2026Updated 2 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,548Jun 1, 2025Updated last year
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,758Jun 20, 2026Updated last month
- 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.
- Graph-based alignment (Hierarchical Graph FM index)☆540Jan 27, 2026Updated 5 months ago
- ncbi-vdb☆103Updated this week
- NGS Language Bindings☆123Dec 6, 2023Updated 2 years ago
- Tools (written in C using htslib) for manipulating next-generation sequencing data☆1,932Updated this week
- bedtools - the swiss army knife for genome arithmetic☆1,041Jun 10, 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.☆1,069Jun 13, 2026Updated last month
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆490Jul 7, 2026Updated 2 weeks ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,583Jul 8, 2026Updated 2 weeks ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,480Jun 29, 2026Updated 3 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment☆918Updated this week
- SPAdes Genome Assembler☆953Jun 16, 2026Updated last month
- Official code repository for GATK versions 4 and up☆1,977Updated this week
- Cutadapt removes adapter sequences from sequencing reads☆586Jun 26, 2026Updated 3 weeks ago
- A fast and sensitive gapped read aligner☆803Jun 1, 2026Updated last month
- parallel fastq-dump wrapper☆308Apr 26, 2023Updated 3 years ago
- Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data☆568Updated this week
- A quality control analysis tool for high throughput sequencing data☆611Updated this week
- The second version of the Kraken taxonomic sequence classification system☆926Jul 9, 2026Updated 2 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Accelerated BLAST compatible local sequence aligner.☆1,312Jul 13, 2026Updated last week
- Near-optimal RNA-Seq quantification☆767Jul 12, 2026Updated last week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆472Updated this week
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆876Apr 20, 2026Updated 3 months ago
- MACS -- Model-based Analysis of ChIP-Seq☆781Jul 7, 2026Updated 2 weeks ago
- Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations☆756Jul 4, 2026Updated 2 weeks ago
- Tools for working with SAM/BAM data☆613Dec 22, 2024Updated last year
- RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.☆311Jun 4, 2026Updated last month
- The next version of bwa-mem☆852Oct 15, 2025Updated 9 months ago
- 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.
- A single molecule sequence assembler for genomes large and small.☆702Jun 18, 2026Updated last month
- A fast multi-threaded k-mer counter☆547Mar 20, 2024Updated 2 years ago
- Tools to process and analyze deep sequencing data.☆762Updated this week
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆561May 15, 2025Updated last year
- Trinity RNA-Seq de novo transcriptome assembly☆895Apr 23, 2026Updated 3 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆865May 2, 2026Updated 2 months ago
- Transcript assembly and quantification for RNA-Seq☆525Jun 3, 2026Updated last month