rrwick / Core-SNP-filter
a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
☆55Updated last week
Alternatives and similar repositories for Core-SNP-filter:
Users that are interested in Core-SNP-filter are comparing it to the libraries listed below
- Recombination-free trees☆56Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆49Updated 6 months ago
- Genome size estimation from long read overlaps☆47Updated last month
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆29Updated 5 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆24Updated this week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- reference-based long read assemblies of bacterial genomes☆47Updated 3 years ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago
- whole genome MLST analysis☆40Updated 8 months ago
- Bacterial GWAS analysis☆35Updated last month
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆41Updated last month
- Fast and space-efficient taxonomic classification of long reads☆43Updated 3 months ago
- Calculate assocations between genes and traits☆20Updated 3 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- Assembly based core SNP alignments☆7Updated last year
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 5 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 9 months ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 6 months ago
- Plasmid analysis using rearrangement distances☆31Updated 2 months ago
- IslandPath standalone software☆31Updated last year
- Colinear block visualisation tool☆30Updated last year
- Gene-flank analysis tool☆26Updated last month
- Predict MLST directly from uncorrected long reads☆26Updated 2 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 9 months ago
- Split Kmer Analysis☆63Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week