Closed winni2k closed 6 years ago
Are you threading through a cleaned de bruijn graph? What species and sequencing platform are you using?
seq=
is the sequence described by the link and it can be calculated from the kmer graph + junction choices in column 4. It is currently required by the links
command when cleaning links. Cleaning links reduces the file size, from which you can strip out the optional columns to further reduce final file size. If I were to re-write several bits of McCortex we could avoid adding seq=
lines to links files, but it would be a lot of work for a small payoff in disk space. I can't imagine many people are generating links that they are not going to then clean. Cleaning is important!
Also worth noting is that increases in kmer size will exponentially decreases the number of links.
Right. Thanks.
My links files are as big as my input fastq files.
I took a look at one of my links files and I saw this:
Kiran tells me
seq
andjuncpos
are not strictly necessary. Would it be possible to add an argument tothread
to suppress the output of these annotations?