HALC: High throughput algorithm for long read error correction

BMC Bioinformatics

Table 3 Evaluation of long read assemblies

Method	N Contigs	N50	Largest contig length	N Covered bases	EPKB
(a) Contigs of A. thaliana
PacBioToCA	1629	27806	110971	51672726	119.4
LSC	1284	29305	105354	40390383	128.6
Proovread	1193	37828	233854	50379300	123.9
CoLoRMap	1324	35477	150127	52913748	113.1
ECTools	1218	40122	182238	56377176	143.5
LoRDEC	1331	28133	104370	40034274	145.1
Jabba	618	29548	87500	22681404	102.1
HALC	1147	44684	296154	54821730	119.9
(b) Contigs of Maylandia zebra
LoRDEC	37460	8878	115008	204752772	121.6
HALC	41434	12062	153787	324763656	92.9

The contigs of tests (a)-(b) are for A. thaliana and Maylandia zebra, respectively. The contigs assembled from the error corrected long reads by PacBioToCA, LSC, Proovread, CoLoRMap, ECTools, LoRDEC, Jabba and HALC are compared in the tests. The performance measurements are listed in the “Performance measurements” section

ISSN: 1471-2105