Assembly of the Pompeii worm's genome (Alvinella pompejana). Genome of Alvinella pompejana

The genome of the Pompeii worm was assembled from an individual collected at 9°50N/EPR and kindly provided by S.C. Cary in 2006. Genome of the Pompeii worm (about 370 Mb) was sequenced from a single individual using both a shotgun and mate-pair 5 kb sequencing using the Illumina HiSeq2500 technology at the A*Star Molecular and Cell Biology Institute. Two replicate runs were performed onto the same individual (2 sets of R1 and R2 compressed files of 33 Go) and used in combination to generate the first genome draft (V1). Paired-end reads libraries (insert size 300bp) were assembled using SOAPdenovo2 (v2.0, -K 41 -d -R), contigs were then scaffolded with OPERA (v1.3.1) using both paired-end (insert size 300bp) and mate pair libraries (insert size 5 kb). Finally, the assembly was gapfilled with Gapcloser (v1.12) to subsequently produce about 3000 scaffolds with a size greater than 15 kb.