Genome assembly
We have followed several step for whole genome assembly of strain SJ98.
- First, we have assembled and annotate the Roche's 454 FLX data with Newbler 2.5.3 assembled, genrated 79 large contigs of 7.85-Mb (Available) and 17 scaffolds of 7.89-Mb size (with 0.74% N bases, where N is unknown). N50 lengths for scaffolds and contigs were 1.32 Mb and 464.6 kb, respectively.
- Second, we have assembled Illumina data separately SOAPdenovo v1.05 and Gapcloser software (at different hash length i.e. K), produced 132 contigs of size 7.92-Mb with N50 contig length of 137,686 nucleotides.
- Third,with the help of Illumina's reads we have reduce the gaps within 17 scaffolds, produced by Roche's 454 from 58,174 to811 gaps by using Gapcloser software.
With the help of Sanger sequencing we have successfully fill 811 gaps remaining within a scaffold and make a genome draft of 14contigs have total size 7.878727 bp (7.9-Mb) with N50 contig length of 1,314,594 bp (~1Mb).
Genome Assembly Sequences Size(bp) N50 Ns GC content(%) Assembly-1* 17 7,894,128 1,315,287 58,174 62.23 Assembly-2** 17 7,884,563 1,314,594 811 62.68 Assembly-3*** 14 7,878,727 1,314,594 0 62.68
* Scaffolds produced by assembly of Roche's 454 FLX data.
** Sequences (16 contigs and 1 scaffold) produced after gap filling of Assembly-1 by Illumina GA IIX data.
***Contigs produced after the finishing of Assembly-3 (Sanger's sequencing and manually by BLAST),final as\ sembly.
We have deposited the assembled genome to GenBank with Accession AJHK00000000.2.