List of bioinformatics pipeline configurations

1 Bioinformatics pipeline configurations

List of all pipeline configurations: The configurations labeled dada_0 and dada_1 refer to the use of the DADA2 tool, where the mergePairs() function was applied with the parameter mismatch=0 or mismatch=1, respectively.
SettingID prep_number process_tool taxonomy
DA1 PREP1 dada_0 idtaxa
DA2 PREP1 dada_0 assigntaxonomy
DA3 PREP1 dada_0 sintax
DA4 PREP1 dada_0 qiime_taxonomy
DA5 PREP1 dada_1 idtaxa
DA6 PREP1 dada_1 assigntaxonomy
DA7 PREP1 dada_1 sintax
DA8 PREP1 dada_1 qiime_taxonomy
DA9 PREP2 dada_0 idtaxa
DA10 PREP2 dada_0 assigntaxonomy
DA11 PREP2 dada_0 sintax
DA12 PREP2 dada_0 qiime_taxonomy
DA13 PREP2 dada_1 idtaxa
DA14 PREP2 dada_1 assigntaxonomy
DA15 PREP2 dada_1 sintax
DA16 PREP2 dada_1 qiime_taxonomy
DA17 PREP3 dada_0 idtaxa
DA18 PREP3 dada_0 assigntaxonomy
DA19 PREP3 dada_0 sintax
DA20 PREP3 dada_0 qiime_taxonomy
DA21 PREP3 dada_1 idtaxa
DA22 PREP3 dada_1 assigntaxonomy
DA23 PREP3 dada_1 sintax
DA24 PREP3 dada_1 qiime_taxonomy
DA25 PREP4 dada_0 idtaxa
DA26 PREP4 dada_0 assigntaxonomy
DA27 PREP4 dada_0 sintax
DA28 PREP4 dada_0 qiime_taxonomy
DA29 PREP4 dada_1 idtaxa
DA30 PREP4 dada_1 assigntaxonomy
DA31 PREP4 dada_1 sintax
DA32 PREP4 dada_1 qiime_taxonomy
DA33 PREP5 dada_0 idtaxa
DA34 PREP5 dada_0 assigntaxonomy
DA35 PREP5 dada_0 sintax
DA36 PREP5 dada_0 qiime_taxonomy
DA37 PREP5 dada_1 idtaxa
DA38 PREP5 dada_1 assigntaxonomy
DA39 PREP5 dada_1 sintax
DA40 PREP5 dada_1 qiime_taxonomy
DA41 PREP6 dada_0 idtaxa
DA42 PREP6 dada_0 assigntaxonomy
DA43 PREP6 dada_0 sintax
DA44 PREP6 dada_0 qiime_taxonomy
DA45 PREP6 dada_1 idtaxa
DA46 PREP6 dada_1 assigntaxonomy
DA47 PREP6 dada_1 sintax
DA48 PREP6 dada_1 qiime_taxonomy
DE1 PREP7 deblur idtaxa
DE2 PREP7 deblur assigntaxonomy
DE3 PREP7 deblur sintax
DE4 PREP7 deblur qiime_taxonomy
DE5 PREP8 deblur idtaxa
DE6 PREP8 deblur assigntaxonomy
DE7 PREP8 deblur sintax
DE8 PREP8 deblur qiime_taxonomy
DE9 PREP9 deblur idtaxa
DE10 PREP9 deblur assigntaxonomy
DE11 PREP9 deblur sintax
DE12 PREP9 deblur qiime_taxonomy
DE13 PREP10 deblur idtaxa
DE14 PREP10 deblur assigntaxonomy
DE15 PREP10 deblur sintax
DE16 PREP10 deblur qiime_taxonomy
DE17 PREP11 deblur idtaxa
DE18 PREP11 deblur assigntaxonomy
DE19 PREP11 deblur sintax
DE20 PREP11 deblur qiime_taxonomy
DE21 PREP12 deblur idtaxa
DE22 PREP12 deblur assigntaxonomy
DE23 PREP12 deblur sintax
DE24 PREP12 deblur qiime_taxonomy
DE25 PREP13 deblur idtaxa
DE26 PREP13 deblur assigntaxonomy
DE27 PREP13 deblur sintax
DE28 PREP13 deblur qiime_taxonomy
DE29 PREP14 deblur idtaxa
DE30 PREP14 deblur assigntaxonomy
DE31 PREP14 deblur sintax
DE32 PREP14 deblur qiime_taxonomy
VU1 PREP7 vsearch idtaxa
VU2 PREP7 vsearch assigntaxonomy
VU3 PREP7 vsearch sintax
VU4 PREP7 vsearch qiime_taxonomy
VU5 PREP8 vsearch idtaxa
VU6 PREP8 vsearch assigntaxonomy
VU7 PREP8 vsearch sintax
VU8 PREP8 vsearch qiime_taxonomy
VU9 PREP9 vsearch idtaxa
VU10 PREP9 vsearch assigntaxonomy
VU11 PREP9 vsearch sintax
VU12 PREP9 vsearch qiime_taxonomy
VU13 PREP10 vsearch idtaxa
VU14 PREP10 vsearch assigntaxonomy
VU15 PREP10 vsearch sintax
VU16 PREP10 vsearch qiime_taxonomy
VU17 PREP11 vsearch idtaxa
VU18 PREP11 vsearch assigntaxonomy
VU19 PREP11 vsearch sintax
VU20 PREP11 vsearch qiime_taxonomy
VU21 PREP12 vsearch idtaxa
VU22 PREP12 vsearch assigntaxonomy
VU23 PREP12 vsearch sintax
VU24 PREP12 vsearch qiime_taxonomy
VU25 PREP13 vsearch idtaxa
VU26 PREP13 vsearch assigntaxonomy
VU27 PREP13 vsearch sintax
VU28 PREP13 vsearch qiime_taxonomy
VU29 PREP14 vsearch idtaxa
VU30 PREP14 vsearch assigntaxonomy
VU31 PREP14 vsearch sintax
VU32 PREP14 vsearch qiime_taxonomy

2 Preprocessing explained

Preprocessing configurations (part 1)
Preprocessing truncLen truncQ maxEE
PREP1 270 2 2
PREP2 270 2 2,5
PREP3 250 2 2
PREP4 250 2 2,5
PREP5 0 2 2
PREP6 0 2 2,5
Preprocessing configurations (part 2)
X1 fastq_trunclen fastq_truncqual fastq_maxee
PREP7 400 20 0.50
PREP8 400 20 0.25
PREP9 400 NAN 0.50
PREP10 400 NAN 0.25
PREP11 420 20 0.50
PREP12 420 20 0.25
PREP13 420 NAN 0.50
PREP14 420 NAN 0.25