Hi all,
I am facing a task which should be really easy to tackle, but I am kind of stuck. Maybe one of you has an idea of how to solve it.
I have a set of contigs (ranging from 2 to 120 kb) coming from a single bacterial species. I would like to assemble these contigs but I know that they do not overlap, i.e. that some parts of the genome are not present in my contigs. I therefore want to map my contigs against a reference genome and then just call a consensus alternative genome from my contigs, where all the gaps are filled with Ns.
I already tried samtools together with vcfutils' vcf2fq but this just outputs the reference genome again.
Here's my command for calling the consensus
So, has anyone an idea which alternative tool I could use to do that?
I also thought about writing my own script and somehow create fake paired end contigs from the information I get mapping the contigs against the reference.
I am facing a task which should be really easy to tackle, but I am kind of stuck. Maybe one of you has an idea of how to solve it.
I have a set of contigs (ranging from 2 to 120 kb) coming from a single bacterial species. I would like to assemble these contigs but I know that they do not overlap, i.e. that some parts of the genome are not present in my contigs. I therefore want to map my contigs against a reference genome and then just call a consensus alternative genome from my contigs, where all the gaps are filled with Ns.
I already tried samtools together with vcfutils' vcf2fq but this just outputs the reference genome again.
Here's my command for calling the consensus
Code:
samtools view -uS sorted.sam |samtools mpileup -uf genome.fasta - | bcftools view -cg - | vcfutils.pl vcf2fq > consensus.fq
I also thought about writing my own script and somehow create fake paired end contigs from the information I get mapping the contigs against the reference.
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