Documentation

SDM option file configuration

This file contains options for the quality filtering of sequences, each option is described again in a comment above the relevant flag (comments can be written in this configuration file by starting the line with "#"). Some options start with a "*". These are relaxed parameters (i.e. they have to be less restrictive) for the secondary quality filter. Sequences in this mid-quality range will not be used for the OTU building, but only mapped to the OTU's.

Flag	Function
minSeqLength	minimal required sequence length AFTER removal of Primers, Barcodes and trimming.
maxSeqLength	maximum sequence length
TruncateSequenceLength	runcate total Sequence length to X (length after Barcode, Adapter and Primer removals), set to -1 to deactivate.
minAvgQuality	minimal required average quality AFTER removal of Primers, Barcodes and trimming.
maxAccumulatedError	Probabilistic max number of accumulated sequencing errors. After this length, the rest of the sequence will be deleted. Complimentary to TrimWindowThreshhold. (-1) deactivates this option.
BinErrorModelMaxExpError, BinErrorModelAlpha	Binomial error model of expected errors per sequence (see Arxiv paper). (BinErrorModelAlpha -1) deactivates this option.
maxAmbiguousNT	maximum ambiguous bases in Sequence
maxHomonucleotide	maximum homonucleotide run length
QualWindowWidth, QualWindowThreshhold	Filter whole sequence if one window of quality scores is below QualWindowThreshhold
TrimWindowWidth, TrimWindowThreshhold	Trim the end of a sequence if a window falls below quality threshhold. Useful for removing low qulaity trailing ends of sequence
keepBarcodeSeq, keepPrimerSeq	keep Barcode / Primer Sequence in the output fasta file - in a normal 16S analysis this should be deactivated (0) for Barcode and deactivated (0) for primer
fastqVersion	set fastqVersion to 1 if you use Sanger, Illumina 1.8+ or NCBI SRA files. Set fastqVersion to 2, if you use Illumina 1.3+ - 1.7+ or Solexa fastq files.
TechnicalAdapter	if one or more files have a technical adapter still included (e.g. TCAG 454) this can be removed by setting this option
TrimStartNTs	delete X NTs (e.g. if the first 5 bases are known to have strange biases)
PEheaderPairFmt	correct PE header format (1/2) this is to accomodate the illumina miSeq paired end annotations 2="@XXX 1:0:4" instead of 1="@XXX/1". Note that the format will be automatically detected
AmpliconShortPE	This option should be "T" if your amplicons are possibly shorter than a read in a paired end sequencing run (e.g. amplicon of 150 in 250x2 miSeq is "T"). This works in conjunction with keepPrimerSeq (should be "F") and the ReversePrimer field in the mapping file.
RejectSeqWithoutRevPrim, RejectSeqWithoutFwdPrim	sets if sequences without a forward (LinkerPrimerSequence) primer will be accepted (T=reject ; F=accept all); default=F
CheckForMixedPairs	this option should be "T" if your run possibly swaps fwd and rev pairs (this can happen depending on how your sequence provider was running illumina).
CheckForReversedSeqs	this option should be "T" if youwant to double check, if sometimes reads are completely reverse-translated.