Hi all,

This code comes from the supp mat of the original paper where we explained how experiments were conducted.

discoSnp (discoSnpRad or discoSnp++) takes as input read files organized in file of files. The idea (described in the documentation) is that a fof contains a list of read files.

The command above is a simple bash for loop, that creates automatically a fof file containing indeed all .fasta of n coli individuals.

More generally, the fof files enable to deal with pair end files, to virtually concatenate read sets, ... Have a look to the documentation.

Have a nice day, Pierre

This is a bash for loop, contaminated with what I think is html code. This code just creates a file called fof.txt, with:

coli_muted_n_30_genome_0_reads.fasta
coli_muted_n_30_genome_1_reads.fasta
coli_muted_n_30_genome_2_reads.fasta
...

There will be $i names, last name is coli_muted_n_30_genome_(i-1)_reads.fasta.

Where did you get this code?