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Table 2 Effects of matching direction and window size on grouping results and time to analyze data using the PSI algorithm.

From: FastGroup: A program to dereplicate libraries of 16S rDNA sequences

Matching

5' Trim

3' Trim

Window

# of Groups

Analysis

Direction

  

Size

 

Time (~min)

5'

1 N in 50 bp

Bact517

10

54

8

3'

1 N in 50 bp

Bact517

10

48

4

5'

1 N in 50 bp

1 N in 50 bp

10

92

12

3'

1 N in 50 bp

1 N in 50 bp

10

94

30

5'

500 bp*

1 N in 50 bp

10

64

5

3'

500 bp*

1 N in 50 bp

10

55

3

3'

1 N in 50 bp

Bact517

5

49

<1

3'

1 N in 50 bp

Bact517

10

48

4

3'

1 N in 50 bp

Bact517

25

51

67

  1. * FastGroup it is not capable of both using a specific number of bp from one end and trimming the other end using one of the other parameters. In these examples, this limitation was circumvented by first trimming the sequences using the 1 N in 50 bp criteria. The output fasta_groups.txt file was then used as the input file for a second FastGroup analysis where 500 bp from the 5' end were used for grouping.