I cannot find the abyss wiki anymore (it is gone) and the github repository says that abyss does have the "se" command for single-end reads. However, the only example I can find where "se" is used for some reason is used in conjunction with multiple libraries (https://github.com/bcgsc/abyss).
I want to know if I can use abyss just to assemble my single-end reads (100bp) only. If I have cleaned/trimmed fastq files for different species, can I just use:
abyss-pe k=50 se="d_r1.fastq"
I would run this command for all my unique species one by one?
I honestly cannot find a clear example of abyss commands for one set of fastq files so I am asking the community!