How to extract genome from iontorent bam file?

Question

[MSRS]

Hi, I hope everything is fine. I have a bam file with the COVID-19 genome from the ion torrent sequencing platform. I want to assemble them and tried with spades, But there is not enough read to form a contig. In that case, I want to assemble them with having gap (NNN). Is there any tools or pipeline?

Thanks In Advance

Answer 1

[5heikki]

No need to assemble, just map the reads on to a reference genome and extract the consensus sequence. If everyone did like this the gisaid dataset would be of much higher quality..

[MSRS]

Thank you, can you please share the code, like align with bwa and then?

Answer 2

[MSRS]

This works for me

bwa mem ref.fa output.fq.gz > alignment.sam
samtools view -bS alignment.sam > aln.bam
samtools sort -m 2G aln.bam -o aln.sorted.bam
samtools mpileup -uf ref.fa aln.sorted.bam | bcftools call -c | vcfutils.pl vcf2fq -d 2 > cons.fa

Thank you

[GenoMax]

Shaminur : You should accept @5heikki's answer as well since that gave you the original clue for how to do this. You are able to accept more than one answer if they work.

[swbarnes2]

Unless you are using a very old version of samtools, you can sort the .sam file, no need to convert it. You really should pipe the output of bwa meme into samtools sort, making a .sam file is usually wasteful.

[MSRS]

Thank you very much for your valuable succession.