cidgoh / bacpaqLinks
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
☆10Updated last month
Alternatives and similar repositories for bacpaq
Users that are interested in bacpaq are comparing it to the libraries listed below
Sorting:
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated 2 years ago
- a broadly applicable tool for automated gene identification and retrieval☆32Updated 7 months ago
- Within-species genome-wide dN/dS estimation from very many genomes☆21Updated 4 years ago
- ZGA prokaryotic genome assembly and annotation pipeline☆12Updated 10 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆25Updated 3 weeks ago
- Quality control plotting for long reads☆10Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- Microbial agile accurate SNP Typer☆30Updated last year
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆46Updated 2 months ago
- Bacterial GWAS analysis☆42Updated last week
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆22Updated 3 months ago
- Genome size estimation from long read overlaps☆58Updated last week
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆39Updated 2 years ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆26Updated 9 months ago
- Intra-species bacterial contamination detection☆25Updated 5 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆46Updated last week
- Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data☆28Updated last week
- Microbial Genome Circular plotting tool for comparative genomics using Circos☆38Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆52Updated 3 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19Updated last year
- Correcting errors in noisy long reads using variation graphs☆51Updated 2 years ago
- Fast and space-efficient taxonomic classification of long reads☆43Updated 2 months ago
- Multi-genome synteny block visualization tool☆42Updated 5 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated 2 months ago
- Genome-Genome circle synteny☆25Updated last year
- a python package for automated generation of phylogenetic trees from genbank files☆22Updated 4 months ago
- Plot genome alignment figure using progressiveMauve & genoPlotR☆22Updated 2 years ago
- Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes☆11Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆24Updated 3 years ago