Use of merqury for illumina paired end reads fot trio binning

[ap1438]

Hi, i wanted to use tools verkko for de novo assembly using trio binning approach.

I have paired end reads from illumina . I was wondering how to use the below commands mentioned in the manual of verkko.

meryl count compress k=30 threads=XX memory=YY maternal.fastq.gz output maternal_compress.k30.meryl meryl count compress k=30 threads=XX memory=YY paternal.fastq.gz output paternal_compress.k30.meryl

So should i just cat the R1 and R2 of paired end reads to genetare a single file for both the parents and then run the command. like cat R1 R2 > Maternal.fastq.gz cat R1 R2 > Paternal.fastq.gz and the use the above command.

Or should i use count forward and count reverse and the union command to generate the maternal_compress.k30.meryl and Paternal_compress.k30.meryl.

[arangrhie]

Hello @ap1438 ,

The script should work as stated using the latest tip version, or come back in a few days as we are fixing the v1.4 release.

meryl count compress k=30 threads=XX memory=YY maternal.*fastq.gz output maternal_compress.k30.meryl
meryl count compress k=30 threads=XX memory=YY paternal.*fastq.gz output paternal_compress.k30.meryl

No need to concatenate. Note memory is in GB. Something like 48 should work fine.

Looping in @brianwalenz here.

[arangrhie]

Use the released Meryl v1.4. No need to concatenate R1 and R2, just provide both in line.