Apologies. This is a question I emailed to you, but it maybe of use to other users if posted here
I would be interested in generating simplitigs from fastq files. This raises a few questions:
1/ As ProPhasm does not accept fastq files would it be suitable to convert the reads directly to fasta or to k-mers before passing to ProPhasm?
2/ There are many potential sources of error/noise in raw reads so would you recommend pre-processing K-mers (filtering/correcting) before passing to ProPhasm?
3/ Would native frequency filtering be something you would consider instituting in the software?
4/ A K-mer size of 32 bp is the maximum allowed for the '-k' option. Could this be relaxed to allow for assembly with larger K-mers and how might this be achieved?
Apologies. This is a question I emailed to you, but it maybe of use to other users if posted here
I would be interested in generating simplitigs from fastq files. This raises a few questions:
1/ As ProPhasm does not accept fastq files would it be suitable to convert the reads directly to fasta or to k-mers before passing to ProPhasm? 2/ There are many potential sources of error/noise in raw reads so would you recommend pre-processing K-mers (filtering/correcting) before passing to ProPhasm? 3/ Would native frequency filtering be something you would consider instituting in the software? 4/ A K-mer size of 32 bp is the maximum allowed for the '-k' option. Could this be relaxed to allow for assembly with larger K-mers and how might this be achieved?
Thanks for your help!