author: Harald Detering
email:  harald.detering@gmail.com

This repository contains a modified version of ART (Illumina only!).
The modified version uses coverage profiles to generate reads with a non-uniform coverage along each reference sequence.

To run, enter:

./art_illumina

you will see in the help text the parameter:

 -cp  --cvgProf  file containing the coverage profile (for uneven read sampling).

which is not part of the original distribution.

The profile can be provided by a FASTA-like file, containing for each sequence:
1. a header line (sequence id must match ref seq id)
2. a line containing the expected coverage at each position, delimited by '#'

So, for example:

>seq1
5#5#5#10#10#10#100#100#100#

would mean the first 3 positions in seq1 each would have a relative weight of 5 to be selected as starting positions for read pairs, the next 3 positions a weight of 10 and the last 3 have a relative weight of 100.

In the code, the modified parts are highlighed by comments, marked with the letters "HD".
The original, unmodified source files are kept in a copy with the suffix ".dist".


For further help, refer to the original README files (README.art*) and the INSTALL file.