Assembly by the metaSPAes from several libraries of paired-end reads with different reads lengths.
Entering edit mode
4 weeks ago
SergFly ▴ 30

Dear forum members. Could you clarify please.

I have two libraries: 2x300 Illumina and 2x150 MGI. These are metagenomic data from different locations in the lake. I want to assemble them into one assembly by metaSPAdes (cross-assembly).

cat R1_300.fq.gz  R1_150.fq.gz  > combine_R1.fq.gz
cat R2_300.fq.gz  R2_150.fq.gz  > combine_R2.fq.gz

Is it possible to do this? Maybe there are specialized programs for combining, so that there are no problems with insert size. metaSPAdes, judging from the manual, support only one library paired-end reads, so the --dataset option will not work. I came across a doubt that reads can be combined using the cat command. How to do it in this situation?

paired illumina metaspades MGI • 212 views

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