robertsmac:clc-assembly-cell-4.0.0beta-mac_64 sr320$ ./clc_ref_assemble_short -o assemblyLT.cas -q /Users/sr320/Dropbox/Public/tmp/s_4_sequence\ trimmed.fastq -d /Users/sr320/Dropbox/Chrome\ Downloads/omykiss_all_contigs.fasta --cpus 2

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robertsmac:clc-assembly-cell-4.0.0beta-mac_64 sr320$ ./clc_novo_assemble -q /Users/sr320/Desktop/s_4_sequence\ trimmed.fastq -o LTdenovo.fasta --cpus 2 -m 300

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  Reference assemble some reads to some reference sequences. Maximum read

  length is 55.

Options:

  -h / --help: Display this message

  -q / --reads: The files following this option are read files. (may be used

     several times)

  -d / --reference: The files following this option are reference files. Fasta

     and GenBank formats are allowed. (may be used several times)

  -o <file> / --output <file>: Give the output assembly file (required)

  -i <file1> <file2> / --interleave <file1> <file2>: Interleave the sequences

     in two files immediately following the "-i" option, alternating between

     the two files when reading the sequences. Only valid for read files. (may

     be used several times).

  -x <n> / --mismatchcost <n>: Set the mismatch cost (range 1 to 3, default 2)

  -g <n> / --gapcost <n>: Set the gap cost (range 1 to 3, default 3)

  -e <n> / --deletioncost <n>: Set the deletion cost in which case the gap cost

     setting only applies to insertions. (range 1 to 3, default 3)

  -c / --colorspace: Use color space when aligning.

  -y <n> / --colorerrorcost <n>: Set the cost of an error in a color when using

     color space. Can only be used with the "-c" option. (range 1 to 3, default

     3)

  -u / --ungapped: Use ungapped alignment (default is gapped alignment)

  -r <mode> / --repeat <mode>: Set the behavior for reads that match more than

     once, i.e. ignore such reads or place them randomly among the valid

     locations (ignore / random) (default random)

  -s <n> / --scorelimit <n>: Set the limit for the score. The limit is defined

     as the number of points below the read length to accept (default is 8 for

     default scoring scheme).

  -n <n> / --movelimit <n>: Move the length limit for short sequences that are

     not aligned. By default it is 22, 26, and 30 for 1, 2, and 3 errors,

     respectively. By using this option, it is lowered by n.

  -p <par> / --paired <par>: Set the paired read mode for the read files

     following this option. (may be used several times)

     par consists of four strings: <mode> <dist_mode> <min_dist> <max_dist>

     mode is ff, fb, bf, bb and sets the relative orientation of read one and

     two in a pair (f = forward, b = backward)

     dist_mode is ss, se, es, ee and sets the place on read one and two to

     measure the distance (s = start, e = end)

     A typical use would be "-p fb ss 180 250" which means that the reads are

     inverted and pointing towards each other. The distance includes both the

     reads and the sequence between them. The distance may be between 180 and

     250, both included.

     To explicitly say that the following reads are not paired, use "no" for

     par, i.e. "-p no".

     For paired end reads split in two files, use the -i option.

  -m <n> / --memory <n>: Set the maximum amount of memory to use as a fraction

     of the available memory (default is 1.0).

  -t <n> / --maxalign <n>: Set the maximum number of alignments to report for

     each read (default is 1).

  -a <mode> / --alignmode <mode>: Set the alignment mode to one of the

     following:

       local: perform local alignment (default)

       global: perform global alignment

       semi-global: perform semi-global alignment

  -f / --forwardonly: Only match reads in the forward direction (cannot be used

     with paired data).

  --cpus <n>: Set the number of cpus to use.

  --no-progress: Disable progress bar.

Examples:

  Reference assembly a single file with reads to a single file with reference

  sequences:

    clc_ref_assemble_short -o assembly.cas -q reads.fasta -d reference.fasta

  Reference assemble reads from two unpaired runs and a paired end run split

  across two files. Use two reference sequences:

    clc_ref_assemble_short -o assembly.cas -q unpaired1.fasta unpaired2.fasta

                         -p fb ss 180 250 -i paired_1.qf paired_2.qf -d

                         reference1.gb reference2.gb