Hi all,
For a recent project, we managed to sequence a microbial biofilm growing on a surface. It was a mixed community composed of both filamentous and single cells. We first sequenced the community as a whole, and then sequenced only the >10 um size fraction, which held almost only the filamentous portion.
I managed to extract 3 genomes from the >10 um size fraction by both applying MetaBAT and by manually selecting contigs that formed isolated clusters (after merging the whole community and size fractionated samples) with VizBin. The analysis of gene markers confirmed that they belonged to two different Proteobacterial classes and I managed to isolate the most closely related genome for each environmental genome.
Now I would like to scaffold my contigs and complete them as much as I can. Both samples were sequenced on an Illumina MiSeq platform with 2x300 bp paired-end reads. I tried by aligning the contigs on their most closely-related genome with CONTIGuator and then trying to close the gaps with GapCloser, but I'm not sure it's the best strategy. What would you suggest me, instead?
Best regards
-MikeT
