De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

Table 1 Summary statistics for individual and merged assemblies

Kmer	Assembly	No. transcripts >100 bp	N50	Mean length	Max length	Total no. bases
21	Initial	33024	844	525	5689	17,354,832
	Representative	29082	786	501	5659	14,561,997
25	Initial	28723	746	491	5689	14,105,603
	Representative	26715	706	474	5659	12,660,658
29	Initial	26236	615	431	5689	11,307,053
	Representative	25016	590	419	5659	10,488,297
33	Initial	23648	488	363	5584	8,591,562
	Representative	22972	469	355	5584	8,148,996
37	Initial	19180	369	311	5111	5,898,486
	Representative	18821	357	301	5111	5,664,511
41	Initial	12230	281	263	5750	3,218,609
	Representative	12090	273	258	5750	3,122,927
Merged		35680	747	479	5750	17,086,468
Final		32911	675	451	5659	14,828,283
Annotated		15965	927	586	5659	9,357,209

For each kmer, data from both the initial Velvet/Oases assembly (Initial), and the assembly containing only one representative transcript from each locus (Representative) are shown. The “Merged” assembly is the result of merging representative assemblies from different kmers using CD-HIT-EST, the “Final” assembly is after potentially misassembled transcripts were removed, and the “Annotated” set only contains transcripts with a significant BLAST match. Kmer = required length of overlap match between two reads in Velvet; N50 = length-weighted median contig length.

ISSN: 1471-2164