I have a question for the community and I wish I have your opinion and some piece of advise about it.
I have a genomic sequence from a plant species on which I mapped Illumina paired reads (2*150 bp). Those reads come from another species from the same genus. Both species are closely-related and I expect some SNP and indels. I perfomed the mapping with BWA.
Now I got the bam file. I wonder if I should do variant calling using the combined
samtools mpileup/bcftools tools or extract the mapped reads and try a de-novo assembly with those reads using
SOAP-denovo2 for instance... In one hand, SOAP will take the insert size into account but it is harder to set. On the other hand, samtools mpileup looks easier to handle but may be less accurate (?) I don't really know...
At the end, I would like to get the genomic sequence of the new species in fasta format.
NB : I prefer not to perform a whole genome assembly since the reads quantity may not be sufficient to get an interesting coverage.
Thanks in advance,