Comments (3)
Hi,
You have to split the Illumina reads into two files (forward and reverse) at the moment Wengan do not handle pairs in a single fastq file. You can split your file using the seqkit with:
seqkit split2 -p 2 sample21_pe.unmapped.fq
https://bioinf.shenwei.me/seqkit/usage/#split2
best,
Alex
from wengan.
thanks, that could have worked, but now I have small reads (less than 60 apparently) so it gives that error now and maybe this won't work. Do you know where can I assemble this illumina reads + pacbio clr reads?
thanks again
from wengan.
Hi,
You have to remove any read shorter than 60bp for running WenganD, the other Wengan modes WengaA and WenganM work with reads < 60bp. Seqkit implements a filter by read length.
Best
Alex
from wengan.
Related Issues (20)
- short read assembly commands HOT 4
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from wengan.