CleanAlignments

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CleanAlignments
Function Alignment
Phase Pre-processing
Standard CLAs PRE, DATA, RUN, GDB, NO_HEADER
Special CLAs GDB, NO_HEADER
Source location ARACHNE_DIR/assemble


The module CleanAlignments is a pre-processing module that cleans up read-to-read alignments. It edits the file aligns.total2 in place.

CleanAlignments removes alignments that match any of the following three criteria:

CleanAlignments is typically run after the ReadsToAligns series, although it is not recommended for use with shorter read types (anything other than Sanger) because of the first bullet point above.

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