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Table 1 List of analysed assemblies

From: Positional bias in variant calls against draft reference assemblies

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

  1. 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
  2. *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]