How to change the minimun length of SQM analysis (200 pb)

[inej90]

Dear all,

I would like to analyse the microbiome of four forage samples using co-assembly and sqm_longreads (as I'm using nanopore sequences; but they have a low mean length (400-600 pb)). I already run the co-assembly mode and I have a lot of unmapped sequences.

Now, I would like to try to change the parameter mimimum length to consider all sequences in both mode analysis without determining the minimum length as it per default is 200 pb. How can I do that?

Thank you in advance.

[fpusan]

sqm_longreads.pl should already considering all sequences regarding of their length (@jtamames correct me if I'm wrong).

For SqueezeMeta.pl the minimum length does not apply to your input nanopore sequences, but to the contigs resulting from assembly (contigs smaller than 200 bp get discarded by default). You can modify this by changing the -contiglen parameter but I wouldn't recommend it.

[inej90]

Thank you Fernando for the quick answer, I think that sqm_longreads.pl doesn't consider the sequences smaller than 200 pb, because once ran, this message appears:

[fpusan]

Ah, right! You can also use the -c parameter in sqm_longreads.pl and set it to a smaller value in case it helps.

[inej90]

Thank you Fernando. You're right, to change the length using sqm_longreads.pl the command will be one of these two arguments:

-c|-readlen : Minimum length of reads (Default: 200)