A collection of command-line tools I wrote to make various repetitive tasks more convenient
☆16Aug 10, 2026Updated 2 months ago
Alternatives and similar repositories for tools
Users that are interested in 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:
- Analyze and simulate Pool-Seq time series data☆18Jun 16, 2022Updated 4 years ago
- Falcon2Fastg is a tool for converting a FALCON assembly to FASTG format to visualize with Bandage☆13May 16, 2016Updated 10 years ago
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Mar 5, 2018Updated 8 years ago
- qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python☆21Sep 20, 2023Updated 3 years ago
- Assessing spectral estimation methods for Electric Network Frequency (ENF) Extraction☆10Jan 10, 2020Updated 6 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- The MafFilter genome alignment processor☆19Aug 27, 2026Updated last month
- Convert sequence IDs between ucsc/refseq/genbank☆16Aug 28, 2018Updated 8 years ago
- ☆17May 22, 2023Updated 3 years ago
- ☆38Apr 14, 2022Updated 4 years ago
- ☆14Oct 27, 2020Updated 5 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- ☆11Mar 4, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- HyPhy tutorials☆11Apr 9, 2018Updated 8 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 11 months ago
- Modern Hopfield layer implementations in Julia☆16Jul 21, 2022Updated 4 years ago
- ☆10Oct 1, 2026Updated last week
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆26Jul 10, 2026Updated 3 months ago
- Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories☆14Mar 29, 2025Updated last year
- A GNN model that executes simplification algorithms used in the layout phase of de novo genome assembly process.☆11May 24, 2021Updated 5 years ago
- xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from …☆11Oct 21, 2020Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆13Dec 3, 2024Updated last year
- ☆24Jun 9, 2017Updated 9 years ago
- ASMNGS18 - 2018 Conference Details☆12Oct 3, 2018Updated 8 years ago
- Bloom filters in Julia☆18Jul 11, 2019Updated 7 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- Linear time detection of Identity by Descent☆13Jul 22, 2011Updated 15 years ago
- ☆12Sep 30, 2026Updated last week
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆25Jul 22, 2026Updated 2 months ago
- A selection of short scripts for analyzing microbial genomes☆14Jun 26, 2018Updated 8 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.
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Mar 10, 2026Updated 7 months ago
- Documentation, guidelines, and policy on contributing to all BioJulia repositories☆17Sep 24, 2026Updated 2 weeks ago
- R package for Enrichment Depletion Logos (EDLogos) and String Logos☆27Dec 12, 2018Updated 7 years ago
- ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequenc…☆12Apr 20, 2022Updated 4 years ago
- Tools to convert to and from vcf format☆14Jun 21, 2017Updated 9 years ago
- waka waka☆18Mar 18, 2021Updated 5 years ago
- Utility Theory for Dummies: An R Tutorial☆19Nov 12, 2020Updated 5 years ago