Import sequences and analyse quality
Error Rate Estimation
Sample Inference
Merging of paired sequences
Construction of ASV table
Chimera Removal
Assign Taxonomy
Create Phyloseq object
Welcome
to
PhyloForgeScript
Import list of paths to FASTQ files (Excel)
Choose Excel File
Browse...
FASTQs
Metadata
Quality Profile Plots
Filtering-Truncating
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Compute the error rate
Which Error Estimation Function would you like to use?
noqualErrfun
loessErrfun
PacBioErrfun
Quality Type
Auto
FastqQuality
SFastqQuality
Parameter 'nbases'
n
Select value:
1e+05
1e+06
1e+07
1e+08
1e+09
1e+10
Randomise?
FALSE
TRUE
Multithread?
Choose a logical or an integer value
Choose
TRUE
FALSE
Integer
Plot the error rate
Choose a Nominal Q value
TRUE
FALSE
Plot the observed error rates as points?
TRUE
FALSE
Plot the input error rates?
FALSE
TRUE
Plot the output error rates?
FALSE
TRUE
Self-consist
FALSE
TRUE
Pool samples?
FALSE
TRUE
pseudo
Multithread?
Choose a logical or an integer value
Choose
TRUE
FALSE
Integer
Choose minOverlap
Choose maxMismatch
Choose returnRejects
FALSE
TRUE
Choose justConcatenate
FALSE
TRUE
Choose trimOverhang
FALSE
TRUE
Order by... ?
abundance
nsamples
NULL
Skip Chimera Removal?
Method
consensus
pooled
per-sample
Multithread?
Choose a logical or an integer value
Choose
TRUE
FALSE
Integer
tryRC
TRUE
FALSE
Multithread?
Choose a logical or an integer value
Choose
TRUE
FALSE
Integer
Report options
Filtering-Truncating
Download filtered FASTQs
Quality Plots
Raw Aggregated plot
Raw Individual plots
Filtered Aggregated plot
Filtered Individual plots
Export R objects
Intermediate outputs: Computed error rates, inferred samples, merged samples, ASV table, ASV table without chimera
Please note that this R object would be PhyloForgeScript-specific: it won't be usable in PhyloForge in any way.
Create PhyloForgeScript_Inputs.RDS
Download PhyloForgeScript_Inputs.RDS