A comparison across non-model animals suggests an optimal sequencing depth for de novotranscriptome assembly

BMC Genomics

Table 1 Assembly Statistics

Organism	Mouse cov-cutoff-3	Mouse cov-cutoff-10	Mouse-Trinity	Chuniphyesmultidentata	Sergestessimilis	Pleuromamma robusta	Dosidicusgigas	Hormiphoracalifornensis	Harmothoeimbricata
Phylum	Chordata	Chordata	Chordata	Cnidaria	Arthropoda	Arthropoda	Mollusca	Ctenophora	Annelida
Tissue	Heart	Heart	Heart	Whole body	Legs	Whole body	Mantle	Whole body	Scale
Raw Reads	82,886,668	82,886,668	82,886,668	103,415,276	93,597,558	64,116,306	60,661,588	64,675,964	75,608,018
Raw GC (%)	51.90	51.90	51.90	42.29	50.74	48.86	39.89	53.71	41.52
Filtered Reads	73,187,048	73,187,048	73,187,048	102,366,438	92,423,904	63,867,922	56,264,099	57,583,204	70,340,105
Assembled Reads	70,000,000	70,000,000	70,000,000	80,000,000	80,000,000	63,867,922	56,264,099	57,583,204	70,340,105
Transcripts	254,215	62,353	85,294	338,254	107,082	196,104	86,897	175,701	191,290
Total Length (Mbp)	293.55	98.84	79.12	314.99	159.59	240.05	143.09	272.23	216.66
Mean (bp)	1,154	1,585	927	931	1,490	1,224	1,646	1,549	1,132
Median (bp)	547	1,119	421	421	837	855	1,026	1,153	689
N50 (bp)	2,364	2,447	1,828	1,854	2,803	1,993	2,876	2,373	1,949
Oases Loci	77,411	20,889	70272	49,831	18,139	22,385	14,227	17,960	21,914
GC (%)	54.08	53.95	53.46	31.24	44.66	45.78	36.55	51.66	40.53

ISSN: 1471-2164