Alignment-based gene expression quantification
☆40Oct 1, 2026Updated last week
Alternatives and similar repositories for squab
Users that are interested in squab are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆22Jul 28, 2022Updated 4 years ago
- ☆14Oct 14, 2020Updated 5 years ago
- Bioinformatics I/O libraries in Rust☆727Updated this week
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated last year
- Command line utility for working with next-generation sequencing files.☆39Jun 24, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Fast and flexible tool for reading, modifying and writing biological sequences☆18Feb 4, 2026Updated 8 months ago
- A very fast interval tree data structure☆137Feb 3, 2025Updated last year
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 7 years ago
- Command line utility for manipulating FASTQ files☆104Sep 22, 2026Updated 2 weeks ago
- Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalabilit…☆89Apr 1, 2024Updated 2 years ago
- Yet Another Chimeric Read Detector☆88Nov 7, 2024Updated last year
- Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)☆58Jan 28, 2023Updated 3 years ago
- Single-Cell RNA-seq pseudo-aligner☆53May 6, 2024Updated 2 years ago
- BAM CIGAR / MD transcoder for compact on-memory representation and quick drawing☆21Jul 19, 2023Updated 3 years 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.
- base-accurate DNA sequence alignments using edlib and mashmap2☆32Feb 15, 2021Updated 5 years ago
- Fast FASTX parsing and k-mer methods in Rust☆214Updated this week
- Rust utility code☆31Feb 9, 2024Updated 2 years ago
- Per-base per-nucleotide depth analysis☆151May 9, 2026Updated 5 months ago
- gia: Genomic Interval Arithmetic☆69Aug 21, 2024Updated 2 years ago
- Pairwise nucleotide alignment benchmark of Rust bindings☆32Jul 27, 2023Updated 3 years ago
- Fast sequence distance estimates☆34Updated this week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)☆11Jan 7, 2024Updated 2 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.
- ☆16Jan 5, 2018Updated 8 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆59Feb 17, 2022Updated 4 years ago
- A better, faster way to count guides in CRISPR screens.☆35Apr 30, 2026Updated 5 months ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Sep 3, 2026Updated last month
- A command line program for large scale buffering between piped programs☆17Nov 19, 2021Updated 4 years ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆264May 13, 2026Updated 4 months ago
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated 2 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆41Dec 20, 2023Updated 2 years ago
- Dadaist2 🟨 Highway to R☆13Mar 7, 2025Updated last year
- 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.
- Hierarchical binned indexed data store for on-disk genomic data.☆13Jan 18, 2025Updated last year
- Pipelines for using T2T genome as a reference☆15Dec 11, 2024Updated last year
- Fast, parallel Rust implementation of Prodigal for prokaryotic gene prediction in microbial genomes☆30Jul 26, 2026Updated 2 months ago
- gap opening realigner for BAM data streams☆18Oct 17, 2012Updated 13 years ago
- Simple and transparent support for compressed files.☆81Sep 23, 2026Updated 2 weeks ago
- Bidirectional WFA (Paper)☆51May 20, 2024Updated 2 years ago
- Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance cal…☆109Mar 13, 2023Updated 3 years ago