Jabba: hybrid error correction for long sequencing reads

Table 2 Results for LoRDEC, proovread and Jabba

	Gain (%)	Accuracy (%)	Error-free (%)	Aligned (%)	Throughput (%)	N50 (bp)
E. coli - simulated short and real long reads - 4.7 Mbp
Uncorrected reads		85.16	0	59.16		13,578
LoRDEC_n	96.46	99.47	13.74	82.16	62.30	4661
LoRDEC	98.83	99.82	79.31	88.95	63.70	7618
proovread	99.64	99.94	89.64	99.57	58.65	5706
Jabba	99.70	99.95	95.70	99.23	57.04	12,760
A. hydrophila—simulated short and simulated long reads: 4.8 Mbp
Uncorrected reads		86.84	0	100		10,421
LoRDEC_n	99.21	99.89	25.29	96.72	94.79	7625
LoRDEC	99.93	99.99	86.74	99.76	95.35	9695
proovread	99.99	99.99	96.53	99.99	95.40	9803
Jabba	99.74	99.96	97.66	99.98	98.04	10,215
S. cerevisiae - simulated short and real long reads: 12.3 Mbp
Uncorrected reads		83.21	1.50	27.99		3969
LoRDEC_n	91.17	98.51	44.02	77.77	21.72	2869
LoRDEC	92.08	98.67	60.82	83.12	30.43	3802
proovread	–	–	–	–	–	–
Jabba	99.87	99.97	98.35	99.93	27.67	8373
O. tauri - real short and real long reads: 13.2 Mbp
Uncorrected reads		83.83	0.05	23.10		7322
LoRDEC_n	91.04	98.55	63.60	85.05	31.43	985
LoRDEC	91.51	98.62	66.76	85.42	31.54	1043
proovread	98.11	99.69	80.28	90.55	26.31	1501
Jabba	99.06	99.84	83.33	93.31	13.81	4183
A. thaliana - simulated short and real long reads: 121 Mbp
Uncorrected reads		83.32	8.00	47.82		14,256
LoRDEC	90.43	98.40	59.35	50.69	46.09	904
proovread	91.11	98.51	69.71	96.66	42.08	7788
Jabba	99.47	99.91	96.67	99.85	39.87	12,647
D. melanogaster—simulated short and real long reads: 122 Mbp
Uncorrected reads		85.70	22.97	41.72		12,478
LoRDEC	89.18	98.45	54.29	49.24	44.78	1119
proovread	97.07	99.58	67.72	98.36	43.49	11,476
Jabba	99.51	99.93	96.24	99.81	38.20	15,553
Jabba_p	99.51	99.93	96.24	99.82	38.22	15,564

Results for proovread on S. cerevisiae have been left out because they did not compute in 3 days. The subscript p indicates that the tool used the reference genome instead of short reads. The subscript n indicates that the tool used uncorrected short reads

ISSN: 1748-7188