CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

Table 3 CLOTU feature comparison with other pipelines

PIPELINE PARAMETERS	CLOTU	QIIME	PANGEA	SCATA	CANGS	WATERS
1. Screening and filtering sequences with tags	Yes	Yes	Yes	Yes	Yes	Yes
2. Screening and filtering sequences with primer pair	Yes	Yes	No	¹FP	Yes	¹FP
3. Screening and filtering sequences with incompatible tags combination	Yes	No	No	No	No	No
4. Screening and filtering sequences with ambiguity	Yes	Yes	Yes	Yes	Yes	²ND
5. Screening and filtering sequences with length criteria	Yes	Yes	Yes	Yes	Yes	Yes
6. Subsequent trimming tags, primers, and adaptors	Yes	³P	No	³P	³P	No
7. Screening and collapsing homopolymers	Yes	No	No	No	No	No
8. Screening and removing exact identical sequences	Yes	No	No	No	Yes	No
9. Clustering programs ⁴	B/C	C/M	MB/C	BL	M	O
10. Removing singletons	Yes	No	No	No	Yes	No
11. BLAST with NCBInr	Yes	Yes	Yes	²ND	Yes	Yes
12. Filtering uncultured hits from BLAST result files	Yes	No	No	²ND	No	No
13. Top hit statistics of BLAST results for each OTUs	Yes	No	No	²ND	No	No
14. Web-service	Yes	No	No	Yes	No	No

Table providing comparable overlapping features with other pipelines QIIME, PANGEA, SCATA, CANGS and WATERS.
¹FP = Forward primer
²ND = Not documented
³P = Trimming of either tags or primer or adaptor but not all.
⁴Clustering program; B = BLASTCLUST, C = CD-HIT, M = MOTHER, MB = MEGABLAST, BL = BLAST and O = OTUHUNTER

ISSN: 1471-2105