New release available now (V1.2.3.2)!

[Rachid]

Hello everyone!

A new release has been posted and is now available on the CLARK website! Code improvement and bug fixes are included in this version (thank you for your continued feedback!).

A new script "makeSummaryTables.sh" generates two spreadsheets to facilitate your analysis of the CLARK report files.

Given a rank r and a minimum abundance level a (i.e., the ratio between the number of reads classified to a taxon and the total number of reads in the report file), in percent, this script produces in the working directory the following report files:
1) "TableSummary_per_Report.csv":

For each report file, this table indicates the number of reads, the number of assigned or classified reads, the proportion of reads classified in percentage, the minimum abundance level used (as a reminder), and the r most dominant taxa/organisms with abundance higher than a (they are ordered by decreasing order of the abundance). The taxa are reported with scientific name and NCBI taxonomy id.

2) "TableSummary_per_Taxon.csv":
For each taxon/organism identified across all the report files, this table indicates the taxonomy id of the taxon, the minimum abundance level used (as a reminder), the number of reports the taxon was found in (within the list of top r taxa with abundance higher than a), and some statistics about the abundance of the taxon (i.e., minimum, maximum, average and standard-deviation in percent).

Thank you all for your interest and please feel free to suggest new features or comments for improving the software!

Cheers,

Rachid