ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

BMC Bioinformatics

Table 4 ContigExtender results on Animal datasets using MetaSPAdes as seed contigs

Contig ID	Library	Meta SPAdes (bp)	Contig Extender (bp)	Gained length (bp)	Gained (%)	Aligned (bp)	Aligned (%)	Viral genome	Genome size (bp)	Gained genome (%)	PRICE (bp)	Kollector (bp)
1	Dog-pool	5521	9826	4305	78	9760	99	uncultured_crAssphage (NC_024711.1)	97,065	4
2	Fish1-pool	2723	7064	4341	159	6878	97	Enterococcus_virus_phiSHEF5 (NC_042023.1)	41,598	10
3	Mosquito-pool20	3074	10,130	7056	230	9699	96	Culex_Iflavi-like_virus_4 (NC_040716.1)	9698	73
4	Mosquito-pool20	3042	10,130	7088	233	9699	96	Culex_Iflavi-like_virus_4 (NC_040716.1)	9698	73
5	Mosquito-pool27	4106	10,095	5989	146	7030	70	Culex_Iflavi-like_virus_4 (NC_040716.1)	9698	62
6	Mosquito-pool27	6011	10,069	4058	68	10,068	100	Alphamesonivirus_1 (NC_015874.1)	20,192	20		6742
7	Mosquito-pool27	5638	10,016	4378	78	9673	97	Culex_Iflavi-like_virus_4 (NC_040574.1)	9698	45	7820
8	Mosquito-pool20	3689	9872	6183	168	9699	98	Culex_Iflavi-like_virus_4 (NC_040716.1)	9698	64
9	Mosquito-pool27	2430	2674	244	10	2626	98	Culex-associated_Tombus-like_virus (NC_040575.1)	2645	9
10	Mosquito-pool27	1786	2131	345	19	2052	96	Hubei_mosquito_virus_4 (NC_032231.1)	4971	7

Columns 3–14 are: 3) seed contig length generated by MetaSPAdes; 4) extended contig length from seed contig; 5) gained length from ContigExtender (column 4 subtracted by column 3); 6) Gained length as percentage of seed contig (column 5 divided by column 3); 7) the largest contiguous segment length of extended contig that are aligned to reference genome; 8) percentage of the alignment segment of the extend contig; 9) reference viral genome; 10) viral genome size; 11) gained length from ContigExtender as percentage of viral genome (column 5 divided by column 10); 12) gained extension by PRICE; 13) gained extension by GenSeed; 14) gained extension by Kollector. Entries in the PRICE, GenSeed, and Kollector columns are blank if they produced no extension

ISSN: 1471-2105