Workflows
MetaShot provides a curated, easy-to-use collection of Nextflow pipelines for metagenomics and microbial genomics. We recommend to specify a pipeline version when running the workflow on your data with the -r parameter, e.g. -r 1.0.0.
Table of contents
Metagenomics
kraken2
metashot/kraken2 is a workflow for the taxonomic classification of reads and the abundance estimation of species in metagenomic samples.
mag-illumina
metashot/mag-illumina is a workflow for the assembly and binning of Illumina sequences from metagenomic samples.
containment
metashot/containment is a workflow for the containment estimation of genomes, proteomes, plasmids and other sequences in sequencing read sets using mash screen.
Prokaryotic genomes
prok-assembly
Assemble prokaryotic isolate genomes from Illumina reads.
prok-quality
metashot/prok-quality is a pipeline for assessing the quality of prokaryotic genomes including the prediction of rRNA and tRNA genes.
prok-classify
metashot/prok-classify is a workflow for assigning objective taxonomic classifications to bacterial and archaeal genomes using GTDB-Tk and the Genome Database Taxonomy GTDB.
prok-annotate
metashot/prok-annotate is a workflow for functional annotation of prokaryotic contigs/genomes.
prok-snp
metashot/prok-snp is a workflow for the identification SNVs (of closely related organisms) and phylogenetic tree inference from prokaryotic isolates.
prok-pan
metashot/prok-pan is a workflow for the pan genome analysis of closely related prokariotic genomes.
Other
aweMAGs
metashot/aweMAGs an automated workflow for large-scale microbial eukaryotic MAGs (metagenome assembled genomes) analysis.