Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
☆13May 15, 2018Updated 8 years ago
Alternatives and similar repositories for contig-puller
Users that are interested in contig-puller are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 4 years ago
- ☆16Jun 21, 2023Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated last year
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆38Updated this week
- 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.
- A set of scripts for calculating pairwise SNP distance☆45Feb 19, 2026Updated 5 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated last month
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 7 months ago
- ☆26Apr 20, 2023Updated 3 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes☆18Dec 1, 2025Updated 7 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆203Jun 10, 2026Updated last month
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆42Feb 9, 2022Updated 4 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.
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Jan 4, 2021Updated 5 years ago
- SEER, reimplemented in python 🐍🔮☆136Mar 24, 2026Updated 4 months ago
- A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.☆17Mar 18, 2025Updated last year
- Renames headers in FASTA file☆13Jun 28, 2017Updated 9 years ago
- Pan-genome wide association studies☆219May 29, 2024Updated 2 years ago
- Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …☆36Oct 17, 2023Updated 2 years ago
- ☆38Apr 14, 2022Updated 4 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Apr 11, 2018Updated 8 years ago
- transposable element typing pipeline☆19Mar 8, 2024Updated 2 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.
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated last year
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- Assembling the cause of phenotypes and genotypes from NGS data☆29Jun 11, 2020Updated 6 years ago
- kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs☆12Apr 27, 2026Updated 2 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- all methods related to Enterobase☆44Sep 4, 2024Updated last year
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 7 months ago
- ☆20Jan 23, 2019Updated 7 years ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆108Feb 6, 2025Updated last year
- 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.
- Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming/sorting contigs and converting FASTQ to FASTA.…☆16Jul 14, 2026Updated last week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- POUTINE: a next-generation homoplasy counting method for genome-wide association studies.☆10Mar 9, 2023Updated 3 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆44Jul 17, 2020Updated 6 years ago
- Taxonomic Classification of Bacteria and Archaea Genomes☆16May 20, 2026Updated 2 months ago
- SPANDx - Comparative genomics for next-generation haploid sequence data☆22Jun 9, 2026Updated last month