Manipulation of unitigs and contigs. Relatively old code from 2014 but might still be useful for some tasks today:
-
compute coverage from a dataset of reads
-
some other hidden features in the source code
tigops coverage -kmer-size [k value] -tigs [unitigs file] -reads [reads file] -out [output file] -name [some_id]
What it does it return the average read k-mer abundance for each sequence of the unitig file. The output will look like:
>[original unitig header] _cov_[coverage value]_ID_[some_id]
[sequence]
you can launch it as many times as the number of reads files you can, each time giving the previous output as input, it will append a "_cov_xxx_ID_yyy" at the end of the fasta header.
For building your project, you should do the following
cd tools/tigops
mkdir build
cd build
cmake ..
make -j 8
Then, you should get a binary holding the name of the project.
Note: the first compilation should take some time since the GATB-CORE library is generated.
Tigops considers only kmers that are unique to the unitig.
Increase the following value in tigops.hpp:
#define span KMER_SPAN(2)