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ProfART is a modified version of ART that uses coverage profiles to sample reads at variable depth
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hdetering/profart
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author: Harald Detering email: [email protected] 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.
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ProfART is a modified version of ART that uses coverage profiles to sample reads at variable depth
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