charcoal demo

This directory (demo/) contains a quick and lightweight demonstration of some of charcoal's features.

If you want to take a look at some output without running it yourself, you can see the summary spreadsheet at ../example-output/demo.combined_summary.csv and see two genome reports, one for a LoombaR bin and one for a TARA bin from Delmont et al., 2019.

To run the demo yourself, execute charcoal run demo/demo.conf from the top-level directory, and then look at the output in output.demo/.

Briefly,

• the LoombaR_2017__SID1050_bax__bin.11.fa.gz could be identified against GTDB release 89 based on k-mers (76% were identifiable (f_ident), and of those, 95% (f_major) belonged to s__Anaeromassilibacillus sp002159845). Approximately 2.8% of the contigs were identified as contaminants based on mismatch at the order level or above, and were removed (column f_removed).
• for TARA_ANE_MAG_00014.fa.gz, we provided a lineage (s__Salipiger thiooxidans) in provided-lineages.csv, and contaminants were removed based on that lineage. Approximately 2.6% of the bases in the original genome were removed based on mismatch at order level or above.
• no matches at all were found for GCF_000005845-subset.fa.gz in the GTDB database, so nothing was done.
• too few of the k-mers in TARA_ANE_MAG_00014.fa.gz could be identified in the GTDB database (f_ident < 0.10), so nothing was done.
• of the identifiable k-mers in TARA_PON_MAG_00084.fa.gz, too few belonged to the major lineage (f_major < 0.20), so nothing was done.