LaborBerlin / score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
☆24Updated 10 months ago
Alternatives and similar repositories for score-assemblies:
Users that are interested in score-assemblies are comparing it to the libraries listed below
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated 3 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- Get microbial sequence data easier and faster☆28Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Remove human reads from a sequencing run☆36Updated 4 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆43Updated last month
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 months ago
- Colinear block visualisation tool☆30Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- Intra-species bacterial contamination detection☆25Updated this week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆30Updated 5 months ago
- Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.☆21Updated 9 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 7 months ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated 11 months ago
- Calculate assocations between genes and traits☆22Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Recombination-free trees☆57Updated last year
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 5 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 4 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆45Updated 2 years ago
- Bacterial GWAS analysis☆36Updated 2 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Generate basic stats for an assembly.☆10Updated 2 years ago