⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
☆258Dec 13, 2025Updated 3 months ago
Alternatives and similar repositories for shovill
Users that are interested in shovill are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Mass screening of contigs for antimicrobial and virulence genes☆481Jan 31, 2026Updated last month
- Rapid haploid variant calling and core genome alignment☆575Dec 12, 2025Updated 3 months ago
- Scan contig files against PubMLST typing schemes☆269Updated this week
- hybrid assembly pipeline for bacterial genomes☆635Jul 25, 2024Updated last year
- "Reads to report" for public health and clinical microbiology☆142Dec 9, 2025Updated 3 months ago
- 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.
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆215Aug 27, 2025Updated 7 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆613Feb 18, 2026Updated last month
- Assemble bacterial isolate genomes from Nanopore reads☆130Jan 22, 2025Updated last year
- Rapid prokaryotic genome annotation☆963Jan 6, 2026Updated 2 months ago
- Create a tree using Mash distances☆184Oct 24, 2023Updated 2 years ago
- Rapid large-scale prokaryote pan genome analysis☆374Nov 3, 2025Updated 4 months ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Mar 21, 2026Updated last week
- Reorients assembled microbial sequences☆136Aug 21, 2025Updated 7 months ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- A scalable bacterial genome assembly, annotation and analysis pipeline☆77Dec 5, 2023Updated 2 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆341Sep 11, 2025Updated 6 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆153Dec 31, 2025Updated 2 months ago
- SKESA assembler☆126Oct 11, 2024Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆172Apr 16, 2025Updated 11 months ago
- A flexible pipeline for complete analysis of bacterial genomes☆501Updated this week
- An updated pipeline for pangenome investigation☆351Jan 15, 2026Updated 2 months ago
- BSR-Based Allele Calling Algorithm☆148Mar 13, 2026Updated 2 weeks ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆357Mar 4, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Fast Whole-Genome Similarity (ANI) Estimation☆450Dec 16, 2025Updated 3 months ago
- Finds SNP sites from a multi-FASTA alignment file☆276Dec 16, 2020Updated 5 years ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆175Feb 26, 2026Updated last month
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆148Jan 9, 2026Updated 2 months ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆121Jan 22, 2025Updated last year
- Making whole bacterial genome sequencing data analysis easy☆113Apr 22, 2025Updated 11 months ago
- Build a partitioned pangenome graph from microbial genomes☆296Updated this week
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆404Updated this week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- SPAdes Genome Assembler☆921Mar 17, 2026Updated last week
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated 2 months ago
- geNomad: Identification of mobile genetic elements☆297Mar 18, 2026Updated last week
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆241Oct 12, 2025Updated 5 months ago
- Long-read metagenomic analysis☆110Oct 10, 2023Updated 2 years ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆131Feb 26, 2024Updated 2 years ago
- Fast genome and metagenome distance estimation using MinHash☆436Sep 19, 2025Updated 6 months ago