maxgmarin / panqc
A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses
☆16Updated 10 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 5 months ago
- Genome size estimation from long read overlaps☆48Updated 2 months ago
- Population analysis PIPEline 🛠🧬☆16Updated this week
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Plasmid analysis using rearrangement distances☆31Updated 3 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆22Updated this week
- TAXnomic Profile Aggregation and STAndardisation☆35Updated 3 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Code to create a PRG from a Multiple Sequence Alignment file☆23Updated 10 months ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated 3 weeks ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆30Updated 5 months ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 7 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated last month
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆24Updated 4 months ago
- Colinear block visualisation tool☆30Updated last year
- Quality control plotting for long reads☆10Updated 9 months ago
- Intra-species bacterial contamination detection☆25Updated last week
- Remove human reads from a sequencing run☆36Updated 4 months ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆12Updated 11 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 7 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆19Updated 2 years ago
- Download NCBI assembly genomes with ftp. rsync, ascp☆11Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆14Updated last year
- Parallel/Homoplasic SNP Finder☆19Updated last year
- transposable element typing pipeline☆17Updated 11 months ago
- ☆41Updated 3 months ago