rpetit3 / fastq-dlView external linksLinks
Download FASTQ files from SRA or ENA repositories.
☆367Feb 1, 2026Updated 2 weeks ago
Alternatives and similar repositories for fastq-dl
Users that are interested in fastq-dl are comparing it to the libraries listed below
Sorting:
- Reorients assembled microbial sequences☆132Aug 21, 2025Updated 5 months ago
- A tool to find sequencing data and metadata from public databases.☆593Aug 13, 2024Updated last year
- Assemble bacterial isolate genomes from Nanopore reads☆127Jan 22, 2025Updated last year
- Genome size estimation from long read overlaps☆80Dec 1, 2025Updated 2 months ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆205Sep 22, 2023Updated 2 years ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆290Feb 3, 2026Updated last week
- Randomly subsample sequencing reads or alignments☆254Feb 9, 2026Updated last week
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆606Feb 9, 2026Updated last week
- A flexible pipeline for complete analysis of bacterial genomes☆499Dec 19, 2025Updated last month
- Tool to plot synteny and structural rearrangements between genomes☆341Apr 7, 2025Updated 10 months ago
- An updated pipeline for pangenome investigation☆341Jan 15, 2026Updated last month
- Remove human reads from a sequencing run☆47Dec 16, 2025Updated 2 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆216Feb 4, 2026Updated last week
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 7 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆173Nov 27, 2025Updated 2 months ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆348Dec 9, 2025Updated 2 months ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆209Updated this week
- A grammar of graphics for comparative genomics☆742Feb 5, 2026Updated last week
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆149Oct 2, 2025Updated 4 months ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated 3 weeks ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 5 months ago
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆457Updated this week
- Create a tree using Mash distances☆182Oct 24, 2023Updated 2 years ago
- Align proteins to genomes with splicing and frameshift☆395Jan 5, 2026Updated last month
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆147Jan 9, 2026Updated last month
- Gene cluster comparison figure generator☆635Dec 22, 2025Updated last month
- Synteny and Rearrangement Identifier☆447Apr 29, 2025Updated 9 months ago
- A genome completeness evaluation tool based on miniprot☆233Sep 18, 2025Updated 4 months ago
- Genome browser and variant annotation☆387Oct 30, 2025Updated 3 months ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆108Dec 11, 2023Updated 2 years ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆176Jan 7, 2026Updated last month
- A list of interesting genome browser and genome visualization programs☆1,047Feb 4, 2026Updated last week
- Strain-level haplotyping for metagenomes with short or long-reads.☆63Apr 10, 2025Updated 10 months ago
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆121Jan 20, 2026Updated 3 weeks ago
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- Rapid haploid variant calling and core genome alignment☆565Dec 12, 2025Updated 2 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 6, 2026Updated last week