did pilon improve my genome?

Question

[vasudhapai]

my doubt is if my sequence has actually improved? refseq is the reference sequence. polished is the output from pilon and contigs.fasta is my file generated from spades. pls help I used the command

Java -Xmx2048m -jar pilon-1.24.jar --genome refseq.fasta --frags sorted bam.bam --output polished --fix all

the sorted bam file is my genome aligned with refseq am doing it correctly?

[Pierre Lindenbaum]

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Answer 1

[colindaven]

You can use QUAST with multiple contig sets (if available, ie through multiple rounds of polishing or different polishing tools).

https://github.com/ablab/quast

Then run multiqc on the dir with results to pick up the comparative number of SNPs and indels per 100kbp pre and post polishing. That will allow you to make a judgement.

Answer 2

[Corentin]

You should have log files from pilon, which indicates the % of corrected bases per contig and other useful metrics.

As mentioned by colindaven, you need to compare the genomes pre and post polishing to judge wether pilon improved your assembly.

You can use Quast to compare contig statistics, BUSCO to assess completeness (but I suspect pilon will not change these values too much) and / or align your assemblies to closely related species, if available.