MEGAN6/MALT

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.

MALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output.

Taxpasta supports the tabular file format generated by MEGAN6's rma2info utility. This utility converts RMA6 files created by both MEGAN6 itself and MALT.

Therefore, if you wish to standardise MEGAN6/MALT output, you must run your RMA6 files through rma2info and supply the output of this tool as input to the taxpasta commands.

Profile Format

Taxpasta expects a two-column, tab-separated file. This is generated either by redirecting the rma2info stdout or the --out parameter. It interprets the columns as containing:

Column Header	Description
taxonomy_id
count1

Note that the file itself does not have any column names.

Example

2   994.0
6   3.0
10  19.0
16  24.0
20  21.0
22  9.0
29  2.0
31  4.0
32  6.0
39  6.0

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1. Value used in standardised profile output ↩