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AstrobioMike
Bioinformatics Tools
After running bit to combine taxonomy, I ended up with more taxa than I had before. i.e. after running bracken, I had about 7000 species, but after running bit, there...
bit-genbank-to-gene-seqs.py takes a genbank file, and writes nucleotides seqs for all genes. check it out ;)
currently the workflow errors and stops if there are no bins
- e.g., to be able to give an estimate stating something like "X% of reads from sample X recruit to the MAGs recovered from sample X" (or put another way,...
as per email request
- contig-level coverage is already generated and provided for individual samples, but that would only include the MAGs from that sample - should make a combined bowtie2 db of all...
right now it reports what percent of the initial sequences were retained, but it'd be nice if it also reported what percent of the initial bases were retained (so it...
one place i have it stored is here: https://osf.io/uhk48/files/osfstorage# - then under mapping-to-all-MAGs/workflow - use the 2 envs from the mg workflow that overlap