Velvet 1.2.10 with FASTQs of different read-lengths AND paired- and single-end?

Genomics101 · 12-30-2013, 05:29 PM

Greetings.

I have been using Velvet 1.2.10 to create de novo assembled contigs with good results using 100bp paired-end reads.

Now I have more and different data, because I have longer reads and because I now trim for quality using Btrim64. As a result, from the two original sets of paired-end reads, 100 and 250bp reads (with 400 and 600 bp insert sizes, respective) I have 4 sets of reads:

Sample1_100bp_R1.fastq.pe
Sample1_100bp_R2.fastq.pe
Sample1_100bp_R1.fastq.se
Sample1_100bp_R2.fastq.se
Sample1_250bp_R1.fastq.pe
Sample1_250bp_R1.fastq.pe
Sample1_250bp_R2.fastq.pe
Sample1_250bp_R1.fastq.se
Sample1_250bp_R2.fastq.se

(The single reads result when the pair is sacrificed in the quality trimming)

I have 3 questions:

Is it possible to combine all of these data for a de novo assembly in Velvet?

Are the 250bp reads still considered short reads or are they long reads?

Is there a problem now that the read-length is no longer consistent due to trimming?

Thanks!

mastal · 12-31-2013, 03:53 AM

Quote:

Originally Posted by Genomics101

Is it possible to combine all of these data for a de novo assembly in Velvet?

Yes. You may have to recompile velvet to run with a larger number of categories, probably 'CATEGORIES=4' .
You should flag your 2 sets of PE reads as -shortPaired and -shortPaired2, respectively.

Quote:

Originally Posted by Genomics101

Are the 250bp reads still considered short reads or are they long reads?

See the discussion about this in the velvet manual,

www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

I think it's probably up to you whether you want to consider them long reads or short reads.

see also this thread in the Velvet mailing list archives:
http://listserver.ebi.ac.uk/pipermai...er/001747.html

Quote:

Originally Posted by Genomics101

Is there a problem now that the read-length is no longer consistent due to trimming?

No.

Genomics101 · 12-31-2013, 07:50 AM

Thanks very much, the Manual for my version of Velvet was unclear about all these points and I very much appreciate your time on this.

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12-30-2013, 05:29 PM	#1
Genomics101 Member Location: Maryland, USA Join Date: May 2012 Posts: 60	Velvet 1.2.10 with FASTQs of different read-lengths AND paired- and single-end? Greetings. I have been using Velvet 1.2.10 to create de novo assembled contigs with good results using 100bp paired-end reads. Now I have more and different data, because I have longer reads and because I now trim for quality using Btrim64. As a result, from the two original sets of paired-end reads, 100 and 250bp reads (with 400 and 600 bp insert sizes, respective) I have 4 sets of reads: Sample1_100bp_R1.fastq.pe Sample1_100bp_R2.fastq.pe Sample1_100bp_R1.fastq.se Sample1_100bp_R2.fastq.se Sample1_250bp_R1.fastq.pe Sample1_250bp_R1.fastq.pe Sample1_250bp_R2.fastq.pe Sample1_250bp_R1.fastq.se Sample1_250bp_R2.fastq.se (The single reads result when the pair is sacrificed in the quality trimming) I have 3 questions: Is it possible to combine all of these data for a de novo assembly in Velvet? Are the 250bp reads still considered short reads or are they long reads? Is there a problem now that the read-length is no longer consistent due to trimming? Thanks!

12-31-2013, 07:50 AM	#3
Genomics101 Member Location: Maryland, USA Join Date: May 2012 Posts: 60	Thanks very much, the Manual for my version of Velvet was unclear about all these points and I very much appreciate your time on this.