OptiDetailedAligns

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OptiDetailedAligns
Function Optical map
Phase Analysis
Standard CLAs PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER
Special CLAs OPTIMAP, SEQUENCE, OUTPUT_DIR, ALLOW_RC, REUSE_LOCATIONS, SUPERS, MIN_QUAL, OPTI_XML, SUPERS_XML, ALIGN_XML
Source location ARACHNE_DIR/optical

The module OptiDetailedAligns performs a multi-pass alignment between an assembly and an optical map. The input optical map must be in Arachne file format; use OpgenMap2Arachne if necessary.

Parameters

Argument name Argument type Default value Meaning
OPTIMAP String opticalMap/optimap.simple The optical map file.
SEQUENCE String CCTNAGG Cutting site sequence.
OUTPUT_DIR String [None] <obsolete>
ALLOW_RC Bool True Allow or suppress rc aligns.
REUSE_LOCATIONS Bool False Allow for more than one scaffold to occupy a single location on the map.
SUPERS String [None] Supers to process.
MIN_QUAL UnsignedInt 40 Minimum consensus quality to call a splice site.
OPTI_XML String optimap.xml Output: the map, reformatted (in SUBDIR).
SUPERS_XML String supers.xml Output: info about the assembly (in SUBDIR).
ALIGN_XML String optialign.xml Output: the alignments (in SUBDIR).

Typically, running with the default parameters results in decent alignments; however, in special cases, one might want to have more control over the aligner, e.g. in case of large-scale segmental duplications, unusually low quality scores etc.

Identifying the cutting site sequence

The original map format contains the name of the enzyme used, e.g. "BsiWI". A quick Google search should find the sequence associated with the enzyme.

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