Options for clc_mapper
CLC Read Mapper
Usage information:
-d / --references Reference database file(s) to use.
-z / --circular Indicate that the following reference file contains circular sequences, eg. -d -z mito.fa.
-n / --indexoutput Save index to file, eg. hg19.idx.
-q / --reads Read file(s) to use, eg. read.fastq.
-p / --paired Set paired parameters, eg. fb ss 50 250.
-i / --interleave Form read pairs by interleaving two files, eg. -i mate1.fastq mate2.fastq.
--type Set technology hint to normal or pacbio (default is normal).
-S / --normaltypelimit Switch to long read mapping for reads beyond this length (default is 500).
-o / --output Resulting alignments, eg. result.cas.
-m / --matchscore Set match score (integer range 1 to 10, default 1).
-x / --mismatchcost Set mismatch cost (integer range 1 to 10, default 2).
-g / --gapcost Set insertion and deletion cost (integer range 1 to 3, default 3).
-G / --gapopen Set affine insertion and deletion open cost (integer from 0 to 10, default 0 (linear)).
-e / --deletioncost Set deletion cost (integer range 1 to 3, default is gapcost).
-E / --deletionopen Set affine deletion open cost (integer from 0 to 10, default is gapopen).
-a / --alignmode Set local or global alignment mode (default local).
-f / --forwardonly Restrict mapping to the forward strand.
-b / --backwardonly Restrict mapping to the backward strand.
-r / --repeat Report random hits for multi-hits or ignore them (default random).
-t / --maxalign Set the maximum number of hits to report for each read (default 1).
-s / --similarity Set similarity score (default 0.8).
-l / --lengthfraction Set length fraction (default 0.5).
--noprogress Hide progress indicator.
--cpus Restrict the number of threads to be used, eg. --cpus 20 (default unlimited).
-M / --mappermemory Restrict the amount of memory (MB) to use during mapping. Overrides --cpus parameter.