Finding chimeric contigs in metagenome
Hi,
I have contigs and read tracking file(.afg file) generated from Meta-velvet for a simulated metagenome. I am looking for chimeric contigs in the generated contigs. One idea which comes to my mind is to map the reads (from .afg file) to contigs and see if, two different read maps back to same contigs, assign that contig as chimeric.
Seeing the format of .afg file I am unable to decode it and hence proceed further. Anyone who has a prior experience working on this, please help. Also if you could suggest any other idea, It would be really helpful.
Thanks
Ashwani
I have contigs and read tracking file(.afg file) generated from Meta-velvet for a simulated metagenome. I am looking for chimeric contigs in the generated contigs. One idea which comes to my mind is to map the reads (from .afg file) to contigs and see if, two different read maps back to same contigs, assign that contig as chimeric.
Seeing the format of .afg file I am unable to decode it and hence proceed further. Anyone who has a prior experience working on this, please help. Also if you could suggest any other idea, It would be really helpful.
Thanks
Ashwani