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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ART_PROFILER_ILLUMINA, Weichun Huang<whduke@gmail.com>
ABOUT
This tool is to create an ART illumina read quality profile from Illumina sequencing data
in multiple fastq or gzipped fastq files
USAGE:
./art_profiler_illumina output_profile_name input_fastq_dir fastq_filename_extension [max_number_threads]
PARAMETERS:
output_profile_name: the name of read quality profile to be generated
input_fastq_dir: the directory of input fastq or zipped fastq files
fastq_filename_extension: fastq or gzipped fastq filename extension
max_number_threads:: maximum number of threads/cores to be used for the run (default: all cores)
EXAMPLES:
1) create hiseq2k profiles from all *.fq.gz in the directory fastq_dat_dir
./art_profiler_illumina HiSeq2k fastq_dat_dir fq.gz
2) create miseq2500 profiles from all *.fq in the directory fastq_dat_dir
./art_profiler_illumina MiSeq250 fastq_dat_dir fq
3) create hiseq1k profiles from all *.fq in the directory fastq_dat_dir using 20 threads
./art_profiler_illumina HiSeq1k fastq_dat_dir fq 20
NOTES:
For paired-end fastq files, e.g., *.fq or *.fq.gz, the filenames of the 1st reads must be *_1.fq/*_1.fq.gz,
or *.1.fq/*.1.fq.gz, and those of the 2nd reads must be *_2.fq/*_2.fq.gz, or *.2.fq/*.2.fq.gz
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