Shore mg
From SHORE wiki
shore mg provides a primitive metagenomic analysis.
Command line options
Usage: shore mg [OPTIONS] [MAP_PATHS]
| Allowed options | ||
| -f, --mappaths=<arg[,...]> | Input directories or files | |
| -o, --outfolder=<arg> | (Default: Mg) | Output directory, will be created |
| --collapse=<arg[:...][,...]> | Collapse any sequence ID not listed here to the next smaller one in the list | |
| --power | Initialize the ID combinations for collapse with the power set of all IDs | |
| --autocollapse=<arg> | Specify *.trans or ref.txt file to automatically collapse to the species level; preprocess must have been run with the --fullheader option; 2nd & 3rd word of fasta headers are taken to be the species name | |
| --make-unique | Make alignments unique before processing | |
| Read filter | ||
| -H, --hits-range=<arg,arg> | Set the allowed range of repetitiveness ('1,1' = nonrep reads) | |
| -M, --mm-range=<arg,arg> | Set the allowed range of mismatches | |
| -N, --read-lengths=<arg[,...]> | Use only reads of the given length(s) | |
| -T, --strand=<arg> | Use only reads from the given strand | |
| --sam-ref=<arg> | Reference sequence for SAM file parsing | |
| --peflags=<arg[,...]> | Use only reads with the given PE flag(s) | |
