Assembly quality analysis

Question

[tothepoint]

We have performed denovo assembly for the pig species. Now we are interested in checking the percentage of assembly mapped over reference available in NCBI. I know BWA can do this but not able to figure out how? Please share your experience I will be grateful to you all.

Answer 1

[Istvan Albert]

I would recommend

QUAST – Quality Assessment Tool for Genome Assemblies

http://quast.sourceforge.net/

[tothepoint]

I tried using QUAST and it gave me a report of GC%, N50, N75, L50, L75 which we already found. Is there any way we can tell how much % of the reads mapped to contigs of reference genome? or Genome Coverage. Any lead will be of great help. Thanks..!!

[Istvan Albert]

quest does exactly that, you have the plot for the genome coverage, etc

basically it generates substantially more information beyond just an N50 stat,

usually you don't even need Quast for N50 as the assembler itself produces that information

Answer 2

[tothepoint]

Found the solution for above mention thread.

After indexing I followed the following steps:

bwa mem -M -R "TAG" pig.fa ref.fa > mapped.sam

samtools view -bS mapped.sam > mapped.bam

Bam files was later sorted:

samtools sort mapped.bam mapped_sort.bam

indexed this file:

samtools index mapped_sort.bam

Run flagstat to find the desired mapping results:

samtools flagstat mapped_sort.bam > mappingat.txt

This text file will have your results saved.

[GenoMax]

While this produces a set of stats they are not necessarily stats about the quality of the assembly (which was your original question).

[tothepoint]

I agree my post was not exactly clear. I tried to explain but gone in different direction. I will try to pinpoint the issue from now onwards. Thanks