Posisition or ID?

[Febri Gunawan]

Hi, my name is Febri. I want to ask about how abyss see the sequences in fastq, is it depends on position or ID? Let me illustrate it

I have two files, the first file contains ABC and the second one contains ACD. How Abyss read that? C will be assembled with D or C will find the other C in wherever it is.

A    A

B    C

C    D

Thank you.
Best regards,

Febri

[Ka Ming Nip]

Hi Febri,

In single-thread mode (ie. `j=1' and/or `np=1'), the two FASTQ files would be read one at a time.
In multi-thread/process mode (ie. `j=2' and/or `np=2'), the two FASTQ files would be read in parallel.

Since reads are broken up into k-mers to generate a de Bruijn k-mer graph, the origin of the k-mers (ie. position within a read file, which read file, which file format, etc.) should not matter.

Hope that helps! :)

Ka Ming

[Febri Gunawan]

Thank you Ka Ming.. :)

Best regards,
Febri