phac-nml / mikrokondo
A simple pipeline for bacterial assembly and quality control
☆15Updated this week
Related projects ⓘ
Alternatives and complementary repositories for mikrokondo
- UPHL's Reference Free Pipeline☆25Updated this week
- Influenza data pipeline to automate genotyping assignment☆21Updated 2 weeks ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated 2 months ago
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆22Updated last week
- Microbial agile accurate SNP Typer☆29Updated 10 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆29Updated last month
- CFSAN Shigella Typing Pipeline☆14Updated last year
- Harmonization of AMR predictor tool outputs☆21Updated last year
- Fast and space-efficient taxonomic classification of long reads☆42Updated 2 weeks ago
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- ☆18Updated last week
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆28Updated 2 months ago
- Intra-species bacterial contamination detection☆22Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated last month
- List and download schemes from pubMLST.org and other BIGSDB servers☆8Updated last month
- REcombination BARcode detector.☆13Updated 7 months ago
- Evaluating Nanopore-based bacterial variant calling☆15Updated last month
- Influenza genome analysis Nextflow workflow☆16Updated last week
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆16Updated 3 months ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆26Updated 4 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆40Updated 4 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆24Updated this week
- Colinear block visualisation tool☆30Updated 9 months ago
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14Updated 6 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- A simple nextflow pipeline for running kraken2 and bracken in a docker container☆20Updated 3 years ago
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Archived - please see updated sccmec tool at link below☆13Updated 2 months ago