Custom Partitioning of Selected Database

Custom Partitioning of Selected Databases

The MTSv pipeline makes use of the GenBank and RefSeq databases. The RefSeq sequences are categorized into the assembly levels ("Complete Genome", "Chromosome", "Scaffold", "Contig"). The acquisition of all assembly levels would require terabytes of storage. By default, genbank and "complete genome" are used for database creation but the ability to acquire sequences from other assembly levels is permitted with the --inclubedb flag followed by a list of desired assembly levels and/or genbank. Please note, mtsv_setup is a command line tool and quotes are need to make "Complete Genome" a single parameter in the list, the parameters themselves are case-insensitive. This flexibility allows the inclusion of draft genomes into a database if desired for the metagenomic analysis. The following steps will create three FM-indices B. cereus, B. anthracis and a combination of them. Using mtsv_setup to focus of only organisms of of interest can speed up the processing of an analysis.

Steps 1a and 1b:

Download database (GenBank, RefSeq Chromosome, RefSeq "Complete Genome"):

 mtsv_setup database --path today --thread 8 --download_only --includedb chromosome "Complete Genome" genbank

The following command would build a FASTA datastore using the only RefSeq sequence data with the assembly level of "Complete Genome" downloaded in the previous command using 4 cores.

 mtsv_setup database --path today --thread 4 --build_only --includedb Chromosome genbank

Step 2:

The formatting convention used can be thought of as a list of set operations between comma separated TaxIDs to include and exclude. For example, a Partition of Bacilli (91061) without B. anthracis (1392) or B. cereus (1396) could be specified with the string "91061-1396,1392". The "-" denotes the difference set operation and can be left out if no exclusion is desired.

The following command would build 3 sets of FM-indices using B. cereus, B. anthracis and a combination of them. Using the complete genome assemblies with 2 cores.

mtsv_setup custom_db --path today --thread 2 --partition 1396 1392 1396,1392 --customdb Chromosome