Required files format

Kmdiff fof

The file must be tab-separated, with controls first:

control1: /path/to/control1_read1.fastq ; /path/to/control1_read2.fastq
control2: /path/to/control2_read1.fastq ; /path/to/control2_read2.fastq
control3: /path/to/control3_SE.fastq
case1: /path/to/case1_read1.fastq ; /path/to/case1_read2.fastq
case2: /path/to/case2_read1.fastq ; /path/to/case2_read2.fastq
case3: path/to/case3_SE.fastq

It can contain single-ends as well as paired-ends.

Snakemake config

In this config file, you can change several parameters:

• the number of threads
• minimum size of unitigs analysed to predict genes.
• max memory used by Bcalm2 (in Mo)

Or change the paths, were the databases are and were the results will be. ❗ It is important that you give absolute paths and use double quotes " ❗.