Skip to main content

Advertisement

Table 1 The performance of Newbler and Newbler-BIGrat in assembling different genomes

From: BIGrat: a repeat resolver for pyrosequencing-based re-sequencing with Newbler

Reference 1 Assembly method Genome size (bp) Contig length (bp) Contig number Contig NG50 2 Contig LG50 3 Gap-filling number 4 Gap-filling length 4
Rice PA64S nuclear BWA-SW 372,317,567 328,243,169 55,092 17,903 4,534 \ \
Newbler   353,856,308 61,922 19,383 5,351 \ \
Newbler-BIGrat   362,123,475 41,838 28,677 3,671 20,084 8,267,167
Acinetobacter baumannnii BWA-SW 3,991,133 3,681,865 133 101,163 14 \ \
Newbler   3,684,532 119 128,034 12 \ \
Newbler-BIGrat   3,717,247 104 173,210 9 15 32,715
Rice PA64S mt BWA-SW 490,673 405,286 5 234,879 1 \ \
Newbler   273,171 104 1,022 13 \ \
Newbler-BIGrat   464,774 1 464,774 1 103 191,603
Rice PA64S cp BWA-SW 134,551 133,024 3 58,368 2 \ \
Newbler   113,344 56 81,038 1 \ \
Newbler-BIGrat   134,156 1 134,156 1 55 20,812
  1. Note:
  2. 1. The rice reference is a set of pseudomolecules from Rice Genome Annotation Project (version 6.1) (http://rice.plantbiology.msu.edu) for nuclear, mt and cp genomes. The Acinetobacter baumannii reference genome is the complete sequence from isolate ACICU (accession number: NC_010611). 2. NG50 is the contig length at which 50% of the total genome length is covered. 3. LG50 is the contig number at which 50% of the total genome length is covered. 4. Comparison between Newbler and Newbler-BIGrat.