fastcat is a single executable with subcommands for FASTQ and BAM summary/statistics workflows. It was originally written to santize and concatenate .fastq(.gz) files, hence the name.
☆54Mar 4, 2026Updated 3 weeks ago
Alternatives and similar repositories for fastcat
Users that are interested in fastcat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Tool to flag foldback and chimeric artifacts in long-read sequence alignment files☆37Jan 21, 2026Updated 2 months ago
- Copy number caller for long read data including SNV utilization☆70Mar 31, 2025Updated 11 months ago
- Tandem repeat expansion detection or genotyping from long-read alignments☆149Nov 24, 2025Updated 4 months ago
- ☆40Dec 15, 2025Updated 3 months ago
- Methylation Phasing for Nanopore Sequencing☆49Mar 5, 2023Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Freddie: Annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing☆16Nov 29, 2022Updated 3 years ago
- ☆31Nov 28, 2024Updated last year
- ☆42Mar 13, 2026Updated 2 weeks ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Feb 3, 2023Updated 3 years ago
- Parakit is a tool to analyze the RCCX module, which contain the CYP21A2 gene, using long sequencing reads.☆14Aug 25, 2025Updated 7 months ago
- MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read M…☆13Jul 2, 2022Updated 3 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last month
- Comparison of multiple long read datasets☆165Dec 2, 2025Updated 3 months ago
- Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA☆29Jun 6, 2024Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- v2.x of the microassembly based somatic variant caller☆23Jul 16, 2025Updated 8 months ago
- Extract modifed base call information from Guppy Fast5 files.☆14Mar 28, 2022Updated 4 years ago
- The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized f…☆14Apr 21, 2023Updated 2 years ago
- Pipeline to convert a haploid assembly into diploid☆111Jan 23, 2025Updated last year
- ☆23Dec 12, 2025Updated 3 months ago
- Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling☆344Updated this week
- Plotting scripts for long read sequencing data☆537Mar 17, 2026Updated last week
- Oxford Nanopore HDF/Fast5 to CRAM conversion tool☆22Dec 30, 2019Updated 6 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- ☆12May 2, 2025Updated 10 months ago
- Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data☆14Dec 24, 2024Updated last year
- quickly filter fastq files by matching sequences to a set of regex patterns☆58Dec 14, 2025Updated 3 months ago
- BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing☆31Sep 15, 2019Updated 6 years ago
- long read RNA-seq quantification☆108Mar 16, 2026Updated last week
- Long read / genome alignment software☆312Dec 16, 2025Updated 3 months ago
- Course materials for an introduction to SARS-CoV-2 sequencing data analysis☆14Aug 15, 2024Updated last year
- Tandem repeat genotyping with long reads☆36Sep 23, 2025Updated 6 months ago
- modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data☆16Apr 29, 2024Updated last year
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- Plotting tools for nanopore methylation data☆95Jul 28, 2025Updated 8 months ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- SV detection tool for nanopore sequence reads☆97Updated this week
- ☆125Feb 22, 2026Updated last month
- ☆17Jul 19, 2024Updated last year
- HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of …☆242Feb 3, 2026Updated last month
- seqfu - Sequece Fastx Utilities☆126Mar 3, 2026Updated 3 weeks ago