w2rap-contigger
An Illumina PE genome contig assembler, can handle large (17Gbp) complex
(hexaploid) genomes.
Depends on the KAT analysis program.
To activate:
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bash
source /local/cluster/kat/activate.sh
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Location and version:
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$ which w2rap-contigger
/local/cluster/kat/bin/w2rap-contigger
$ w2rap-contigger --version
w2rap-contigger --version
Welcome to w2rap-contigger
w2rap-contigger version: 0.1
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help message:
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$ w2rap-contigger --help
w2rap-contigger --help
Welcome to w2rap-contigger
USAGE:
w2rap-contigger [-h] [--version] [-t <int>] [-m <int>] -r <file1.fastq
,file2.fastq> -o <string> -p <string> [-K <60|64|72|80
|84|88|96|100|108|116|128|136|144|152|160|168|172|180
|188|192|196|200|208|216|224|232|240|260|280|300|320
|368|400|440|460|500|544|640>] [--from_step <1|2|3|4|5
|6|7>] [--to_step <1|2|3|4|5|6|7>] [-d <int>]
[--tmp_dir <string>] [-s <int>] [--min_freq <int>]
[--min_qual <int>] [--pair_sample <int>]
[--extend_paths <bool>] [--path_finder <bool>]
[--dump_all <bool>] [--dump_perf <bool>] [--dump_pf
<bool>] [--dev_run_test <devel only>]
Where:
-h, --help
Displays usage information and exits.
--version
Displays version information and exits.
-t <int>, --threads <int>
Number of threads on parallel sections (default: 4)
-m <int>, --max_mem <int>
Maximum memory in GB (soft limit, impacts performance, default 10000)
-r <file1.fastq,file2.fastq>, --read_files <file1.fastq,file2.fastq>
(required) Input sequences (reads) files
-o <string>, --out_dir <string>
(required) Output dir path
-p <string>, --prefix <string>
(required) Prefix for the output files
-K <60|64|72|80|84|88|96|100|108|116|128|136|144|152|160|168|172|180|188
|192|196|200|208|216|224|232|240|260|280|300|320|368|400|440|460|500
|544|640>, --large_k <60|64|72|80|84|88|96|100|108|116|128|136|144
|152|160|168|172|180|188|192|196|200|208|216|224|232|240|260|280|300
|320|368|400|440|460|500|544|640>
Large k (default: 200)
--from_step <1|2|3|4|5|6|7>
Start on step (default: 1)
--to_step <1|2|3|4|5|6|7>
Stop after step (default: 7)
-d <int>, --disk_batches <int>
number of disk batches for step2 (default: 0, 0->in memory)
--tmp_dir <string>
tmp dir for step2 disk batches (default: workdir)
-s <int>, --min_size <int>
Min size of disconnected elements on large_k graph (in kmers, default:
0=no min)
--min_freq <int>
minimum frequency for small k-mers on step 2 (default: 4)
--min_qual <int>
minimum quality for small k-mers on step 2 (default: 7)
--pair_sample <int>
max number of read pairs to use in local assemblies on step 5(default:
200)
--extend_paths <bool>
Enable extend paths on repath (experimental)
--path_finder <bool>
Run PathFinder (experimental)
--dump_all <bool>
Dump all intermediate files
--dump_perf <bool>
Dump performance info (devel)
--dump_pf <bool>
Dump pathfinder info (devel)
--dev_run_test <devel only>
runs development tests
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software ref: https://github.com/bioinfologics/w2rap-contigger
research ref: