Hi everyone,

I'm working on a study about soil metagenomics and needless to say I'm relatively new to all of this. I read from multiple sources that it is recommendable to merge the paired end files (MiSeq amplicon sequencing) with PEAR before assembling them with megahit.

I successfully merged the files with PEAR and go the following output:

• Sample.assembled.fastq
• Sample.discarded.fastq (always empty)
• Sample.unassembled.forward.fastq
• Sample.unassembled.reverse.fastq

So those are basically 1 single end and two paired end files, correct? Should I work with all three of them or can I discard the unassembled files?

The megahit syntax is the following:

megahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries

So in my case:

megahit -r Sample.assembled.fastq -o out

Or should I include all 3 files?

megahit -1 Sample.unassembled.forward.fastq -2 Sample.unassembled.reverse.fastq -r Sample.assembled.fastq -o out

I would highly appreciate it if someone could shed some light on it. Thank you very much.