ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

Table 1 ALLPATHS, Velvet and EULER assemblies of five microbial genomes: source data

	S. aureus	E. coli	R. sphaeroides	S. pombe	N. crassa
Source data
Strain	USA300	K12 MG1655	2.4.1	972 h	74A
Reference sequence	Finished, curated	Finished, curated	Finished, curated	Finished	Finished
GC composition (%)	33	51	69	36	49
Genome size (kb)	2,873	4,639	4,603	12,554	39,226
Reference N50 (kb)	2,873	4,639	3,188	4,509	665
Sequence coverage (x)	89	139	370	148	123

For five genomes, statistics from ALLPATHS, Velvet, and EULER assemblies are shown. In all cases identical data were supplied to both programs. Contigs of size <1,000 bases were discarded. Strain: strain that was sequenced. GC composition: percent of GC base pairs in the finished reference sequence. Genome size: total number of bases in reference. Reference N50: N50 size of reference. Reference sequences: all were finished, and in addition the reference sequences for the three bacterial genomes were curated to ensure full concordance with the samples, as described in the main text. S. aureus, circular chromosome and two plasmids; E. coli, circular chromosome; R. sphaeroides, finished but differs at 374 base positions from our sample, two circular chromosomes, four circular plasmids, and one linear plasmid; S. pombe, three linear chromosomes; N. crassa, finished at the base level, 251 contigs from 7 chromosomes. Sequence coverage: total coverage by usable reads; for a precise definition see Table S3 in Additional data file 1.

ISSN: 1474-760X