concationation

[smangul1]

Can you please upload script to concatenate genomes here on github

Also create a separate wiki page to put the location of datasets and BWa indexes for concatenated file

[mealser]

This part is already uploaded to github:
https://github.com/smangul1/miCoP/blob/master/CoveragePlot/ConcatContigs.py

to run the code use the following:
awk -F "|" '{print $2}' fungi.names | uniq > RefList.txt
python ConcatContigs.py RefList.txt fungi.fa > fungi_ConcatContigs.fa

[mealser]

Please note that i change the content of the first line of each contig sequence for the output file such that it includes (1) the name of the organism rather than the name of the contig. (2) the length of the new concatenated contigs rather than the length of the contig..