mSWEEP User Manual
This document details how to use the rust port / rewrite of mSWEEP, available at https://codeberg.org/themaklin/msweep-rs.
msweep-rs incorporates the functionality of both mSWEEP and mGEMS. The tool also provides a method for quality checking the binned reads, inspired by demix_check.
Tools comprising the pipeline
See installation for recommended ways to obtain these.
Abundance estimation and binning
- msweep-rs
This manual does not cover the C++ mSWEEP/mGEMS packages.
Pseudoalignment
One of
Themisto is recommended for indexes that are sparse, eg. those containing multiple species.
Fulgor is recommended for indexes that are dense, eg. containing many assemblies from a single species.
Both tools can be used for either case. The results may vary slightly due to differences in the algorithms they use.
Metagraph and Bifrost are supported but not recommended. Alignments in the SAM format are also supported but must be processed with ahda.
Using the pseudoalignment outputs
msweep-rs can natively read input from either, but it is recommended to use ahda to compress the results for better I/O performance and to save disk space.
Defining target groups/clusters
PopPUNK is recommended for clustering the reference assemblies.