metaT mapping -- rm ribosomal reads

remove ribosomal reads from metaT data

changed milestone to %Analyses

added Analysis Enhancement Investigation Tool labels

added Somewhere over the rainbow label

changed milestone to %Stretch goal

removed Tool label

SortMeRNA

Very inefficient and slow - does not use all cores, requires >12 hours for GDB sample (cancelled before finishing). Appears to be a known issue.

changed the description

changed milestone to %Analyses

removed Somewhere over the rainbow label

mentioned in commit 3cc031ec

infernal

PMC6754622: "ALTERNATE PROTOCOL 1: USING Rfam AND Infernal FOR RNA SEQUENCE ANALYSIS OF NUCLEOTIDE SEQUENCE DATASETS"

wget ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz
wget ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.clanin
gunzip Rfam.cm.gz
# infernal (1.1.2, h516909a_3, from bioconda)
cmpress Rfam.cm

Not cool either:

• input can only be FASTA files
• output is hmmer output, i.e. out and tblout

I.e. requires pre- and postprocessing

bbmap

Suggested here and here.

mentioned in commit ffdcc3aa

mentioned in commit 7fc7f4d1

Closing as bbmap/bbduk seems to be a good solution.

closed