Assemblator

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For the script module, see Assemblez.
For the deprecated script module, see Assemble.
Assemblator
Function Assembly
Phase Assembly
Standard CLAs PRE, DATA, RUN, GDB, NO_HEADER
Special CLAs HYPCONTIG_FILE, COMPRESSED_ALIGNS, MIN_OVERLAP, N_HAPLOTYPES, EXPLICIT_SEED, MIN_INI_LAP, MAX_NEG_GAP, MAX_OVERLAP, BUILD_ALL, EXCLUDE_DIR, VALID_READS, BUILD_SUPERS, TWO_PASS_TWO_HAPS, EXPECTED_COVERAGE, DONT_ADD_SUBSUMED, MIN_INSERT_SIZE, MAX_INSERT_SIZE, USE_REPETITIVE_READS
Source location ARACHNE_DIR/ueberal

Assemblator is an early assembly module, typically the first to be run in scripts. It performs the consensus algorithm: a preliminary grouping of reads into contig consensus, based on the alignments that have been created during pre-processing (in the file aligns.total2.) It is tentative, avoiding repetitive reads. It does not create supercontigs.

The output of Assemblator is a hypcontig file, which must be converted to Arachne binary format with ConvertToArachne before it can be used further.

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