maxgmarin / panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
☆16Updated 9 months ago
Alternatives and similar repositories for panqc:
Users that are interested in panqc are comparing it to the libraries listed below
- Genomewide Epistasis Analysis on Bacteria☆14Updated 4 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆41Updated last month
- Genome size estimation from long read overlaps☆47Updated last month
- Microbial agile accurate SNP Typer☆29Updated last year
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆29Updated 4 months ago
- Strain-level taxonomic classification of metagenomic data using pangenome graphs☆22Updated last month
- Plasmid analysis using rearrangement distances☆31Updated 2 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆48Updated 6 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆18Updated 2 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Remove human reads from a sequencing run☆35Updated 3 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 6 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆23Updated last year
- Calculate assocations between genes and traits☆20Updated 2 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆41Updated 3 weeks ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 4 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆34Updated last month
- genomic alignment similarity search tool☆19Updated 7 months ago
- ☆21Updated 4 months ago
- ContScout sequence contamination filter tool☆19Updated this week
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated last month
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆30Updated last month
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆11Updated 10 months ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 5 years ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated 2 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆22Updated 8 months ago