Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken
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Updated
Dec 4, 2020 - Nextflow
Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken
Simulate a microbial pathogen outbreak dataset for use in variant-calling validations
Simulate genomic variation, based on input reference genomes
Nextflow pipeline for estimation of evolutionary rate using Bayesian statistics.
A workflow for assessing similarity between a set of plasmid sequences
Collect basic sequence QC metrics from nanopore reads
Demultiplex nanopore reads and combine into a single file per sample
A pipeline for bioinformatics analysis of bacterial genomes
Nextflow wrapper for the dragonflye assembler, with additional QC
Generate simulated oxford nanopore reads from a reference sequence
A cgMLST pipeline based on the KMA aligner
Perform read mapping and variant calling using snippy
Run mlst on multiple samples with integrated quality control.
Pipeline to perform alignment & variant calling on whole-genome sequence data
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