How to identify used and unused reads for an assembly performed with Abyss

Question

[abseq]

Hi, All

I am doing de novo assembly in ABySS and i got the result. Now I want to know how many reads are assembled and how many are not?

Can anyone help me to find out?

Thanks in advance.

[Prakki Rama]

I think there is no direct option in abyss to do that. We have to map the reads on to the assembly using bowtie2 or bwa, create a sam or bam file. Using samtools flagstats, you can find the number of reads used in the assembly.

[abseq]

Thank you Prakki Rama