Table 1

Results and characteristics of assemblies run with different parameter settings.

Gap Penalty

30

50


Match %

Match length

Number of contigs and average length

Number of assembled reads

Number of contigs and average length

Number of assembled reads


85%

19

50,689 (537)

255,711

51,058 (533)

252,299

23

49,621 (516)

248,537

50,039 (513)

245,563

25

48,962 (507)

244,120

49,366 (504)

241,289


90%

19

55,886 (499)

220,517

55,996 (497)

217,169

23

53,724 (490)

213,344

53,824 (488)

209,916

25

52,770 (485)

209,735

52,726 (483)

206,167


95%

19

51,289 (443)

156,578

51,908 (441)

154,605

23

46,611 (441)

142,428

46,585 (439)

140,071

25

44,752 (439)

137,096

44,674 (437)

134,566


Combination of reference-based (match % = 88) and de novo assemblies (match % = 93)

88%,93%

19

63,687 (500)

225,517


Results from assemblies run in Seqman Ngen with different starting values for gap penalty, minimum match size, and mimimum match percentage. We present the number of contigs, average contig size (in parentheses), and the number of reads assembled into contigs for each different set of parameter settings.

Parchman et al. BMC Genomics 2010 11:180   doi:10.1186/1471-2164-11-180

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