RemoveContigs

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RemoveContigs
Function Cleanup
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, OUTDIR, GDB, NO_HEADER
Special CLAs MIN_READS, MIN_LENGTH
Source location ARACHNE_DIR/assemble_alt

The module RemoveContigs removes insufficiently large contigs from an assembly. The size threshold is defined by the command-line arguments MIN_READS and MIN_LENGTH, which specify respectively the number of reads a contig must be aligned to, and its minimum length in bases, in order to survive. You must specify at least one of these arguments. If you specify both, RemoveContigs will require contigs to meet both thresholds.

RemoveContigs may cause supercontigs to become disconnected.

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