Reads | Identifier | Assembler | Pos | k |
---|
Bcon | abyss_9C | ABySS | 80 | 80 |
Bcon | merac_6C | Meraculous | 71 | NA |
Bcon | phus_5C | Phusion | 78 | NA |
Bcon | sga_7C | SGA | 121 | NA |
Bcon | soap* | SOAPdenovo2 | 36 | 36 |
Mzeb | abyss_7C | ABySS | 56 | 56 |
Mzeb | allp_6C | ALLPATHS-LG | 96 | 96 |
Mzeb | soap_11E | SOAPdenovo2 | 46 | 46 |
Sim | allp | ALLPATHS-LG | 96 | 96 |
Sim | sga_m75 | SGA | 100 | NA |
Sim | sga_m77 | SGA | 100 | NA |
Sim | soap_K69 | SOAPdenovo2 | 70 | 70 |
Sim | soap_K71 | SOAPdenovo2 | 72 | 72 |
- This study focused on a subset of the B. constrictor (Bcon) and M. zebra (Mzeb) genome assemblies submitted by the assembler developers to the Assemblathon 2 competition. In addition, we simulated reads from A. thaliana chromosomes 1 and 2 (Sim) and constructed several assemblies with varying parameters. For SGA, we varied the minimum string overlap (-m 75 and -m 77 for sga_m75 and sga_m77 respectively). For SOAPdenovo2, we set the -K parameter to 69 and 71, which corresponded to k = 70 and 72 for soap_K69 and soap_K71 respectively. ‘Pos’ column shows the position (counted from ends of contigs or scaffolds) where variants occur most frequently. ‘NA’ in the ‘k’ column indicates that the choice of k was not reported and could not be determined from other sources
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*The Bcon assembly by the SOAPdenovo2 team submitted for the competition was assembled using an incorrectly labelled library. We analysed the corrected version that was constructed after the competition [17]