Compute coverage and percent GC

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Compute coverage and percent GC

This module performs six small tasks with the fasta file of the assembled contigs: (1) It parses the sequencing coverage calculated by the assembler from the fasta header lines; (2) It computes the percent GC value for each contig from the contig sequence; (3) It sorts the contigs by length; (4) It transcribes all sequence data to uppercase
Filters raw sequencing reads in a fastq or fasta file; (5) It transcribes all ambiguous bases to "N". Uppercase and N's are required by some external programs used by downstream modules; (6) It predicts open reading frames and computes coding density for each contig.

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Runtime

Minutes.

External dependencies

This module requires prodigal for predicting open reading frames to compute coding density.

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Parameters (type, default)

• Average read length (setAverageReadLength, int, 100): Some assemblers only provide the number of reads for each contig, rather than the coverage.

• Number of reads regexp (setRegexpNumberOfReads, String, "(?:(?:numreads)|(?:read_count))[=_](\d+)"): The regular expression used to parse the number of reads for a contig from the fasta header file. The default usually works.

• Coverage regexp (setRegexpCoverage, String, "co*vg*[a-z]*?[=_]([\d.]+)"): The regular expression used to parse the sequencing coverage for a contig from the fasta header file. The default usually works.

• Set processors used (setProcessorsUsed, int, 4): The number of processors/cores/threads used for computations.

• Set temp folder (setTempFolder, String, "/temp/metawatt"): Temp folder used for intermediate files.

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Files generated

• ./output/[assemblyfilename].properties.txt: Listing of all contigs and their inferred properties.