Question: How to identify used and unused reads for an assembly performed with Abyss
gravatar for ab
5.3 years ago by
ab0 wrote:

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.

abyss tool assembly • 1.2k views
ADD COMMENTlink modified 5.2 years ago • written 5.3 years ago by ab0

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.

ADD REPLYlink written 5.2 years ago by Prakki Rama2.3k

Thank you Prakki Rama

ADD REPLYlink written 5.2 years ago by ab0
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