Hi Peter, it turns out we only have a workbench licence, the clc_assembler packaged with the workbench is called ./clc_assembler_ilo
which has the man page below, do you think this is the same binary as the clc-assembly-cell assembler?
usage: clc_assembler [options]
Assemble some reads and output contig sequences in fasta format.
-h / --help: Display this message
-q / --reads: The files following this option are read files. Fasta, fastq,
and sff formats are allowed. (may be used several times)
-i <file1> <file2> / --interleave <file1> <file2>: Interleave the sequences
in two files, alternating between the files when reading the
sequences. Only valid for read files. (may be used several times)
-o <file> / --output <file>: Give the output fasta file (required)
-f <file> / --feature_output <file>: Output scaffolding annotation in
GFF (default) or AGP format. The file suffix is used to determine the
output format. Use '.gff' for GFF format and '.agp' for AGP format.
-m <n> / --min-length <n>: Set the minimum contig/scaffold length to output
(default = 200)
-w <n> / --wordsize <n>: Set the word size for the de Bruijn graph (default
is automatic based on input data size)
-b <n> / --bubblesize <n>: Set the maximum bubble size for the de Bruijn graph
(default is 50)
--cpus <n>: Set the number of cpus to use.
-v / --verbose: Output various information while running.
-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.
It is also allowed to insert a "d" before the mode. This indicates that
the reads in the following file(s) should only be used for their paired end
information and not to build initial contigs. E.g. "-p d fb ss 180 250".
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.
-e <file> / --estimatedistances <file> Estimate paired distances for all paired
reads and save the distance estimates in <file>. If it is not possible to
get an accurate distance estimate for a file, the original paired distance
-g <mode> / --fragmentmode <mode>: Set the mode for how reads are used to
create fragments. One mode is "ignore", which ignores the nucleotides
when building initial fragments. The other mode is "use", which uses
the nucleotides when building initial fragments. This is the default mode.
The mode applies to all read files following this option. The option may be
-n / --no-scaffolding: Pair info is used for contig creation, but no
scaffolding is performed.
Assembly of a single file with reads:
clc_assembler -o contigs.fasta -q reads.fasta
Assembly of two interleaved files with paired end reads:
clc_assembler -o contigs.fasta -p fb ss 180 250 -q -i reads1.fq reads2.fq