Question: How to identify used and unused reads for an assembly performed with Abyss
gravatar for amitbikram87
4.7 years ago by
amitbikram870 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 • 1.1k views
ADD COMMENTlink modified 4.6 years ago • written 4.7 years ago by amitbikram870

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 4.6 years ago by Prakki Rama2.2k

Thank you Prakki Rama

ADD REPLYlink written 4.6 years ago by amitbikram870
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1093 users visited in the last hour