Computational workflow for the fine-grained analysis of metagenomic samples

BMC Genomics

Table 1 Before-and-after extension example of a read with two candidate fragments to be joined

Before extension of local or ungapped alignments
029701.102903 — NC_004663.1 — Bacteroides thetaiotaomicron 897405
N	SCORE	IDEN	LEN	SIM	IGAPS	EGAPS	STRA	R1	R2	G1	G2
1	-	134	145	84	0	0	Plus ∖Plus	1	133	1631420	1631563
2	-	94	104	80	0	0	Plus ∖Plus	147	249	1631564	1631666
After extension (“glocal-like” alignment)
029701.102903 — NC_004663.1 — Bacteroides thetaiotaomicron 897405
1	-	224	248	90	1	2	Plus ∖Plus	2	249	1631420	1631665

In the top, the table before extension. Fragments (1) and (2) are separated by a relatively small gap of 14 base pairs (The ending read coordinate R2 of (1) is 14 base pairs away from R1 in (2)). These fragments represent an example of candidate fragments. The after subtable (bottom) displays the resulting extended fragment and shows a longer alignment with still high similarity and a low number of gaps (one opening gap and two extension gaps). The score is calculated afterwards (See “New score and expected value calculation”).

ISSN: 1471-2164