| UC-ECHO(1) | User Commands | UC-ECHO(1) |
NAME¶
uc-echo - Short-read Error Correction
SYNOPSIS¶
uc-echo [options] read_file_name
OPTIONS¶
- -h, --help
- show this help message and exit
- -o OUTPUT_FILENAME, --output=OUTPUT_FILENAME
- Output file name
- -l LOG_FILENAME, --log=LOG_FILENAME
- Log file name
- --DD=TMP_DIRECTORY, --tmp_dir=TMP_DIRECTORY
- Temporary data directory
- -u NCPU, --ncpu=NCPU
- Number of processes used in training
- -b BSIZE, --block_size=BSIZE
- Split data into blocks of specified size
- --nh=NHASH, --n_hash_block=NHASH
- Split hash table into n tables
- --rm=READ_MERGE, --read_merge_size=READ_MERGE
- Merge n hash tables at a time
- --hm=HASH_MERGE, --hash_merge_batch_size=HASH_MERGE
- Merge n adjacency lists at a time
- -k K, --kmer=K
- k-mer size used for hashing
- -e E, --min_error_tolerance=E
- Minimum error tolerance for parameter searching
- -E E, --max_error_tolerance=E
- Maximum error tolerance for parameter searching
- --hh=H, --min_minimum_overlap=H
- Minimum minimum overlap length for parameter searching
- --hH=H, --max_minimum_overlap=H
- Maximum minimum overlap length for parameter searching
- --h_rate=H_RATE, --heterozygous_rate=H_RATE
- Rate for heterozygous site
- --model_selection_size=MSIZE
- Model selection data set size
- --keep_all_files
- Keep all temporary files. By default, temporary files are deleted automatically.
- -h, --help
- show this help message and exit
- -o OUTPUT_FILENAME, --output=OUTPUT_FILENAME
- Output file name
- -l LOG_FILENAME, --log=LOG_FILENAME
- Log file name
- --DD=TMP_DIRECTORY, --tmp_dir=TMP_DIRECTORY
- Temporary data directory
- -u NCPU, --ncpu=NCPU
- Number of processes used in training
- -b BSIZE, --block_size=BSIZE
- Split data into blocks of specified size
- --nh=NHASH, --n_hash_block=NHASH
- Split hash table into n tables
- --rm=READ_MERGE, --read_merge_size=READ_MERGE
- Merge n hash tables at a time
- --hm=HASH_MERGE, --hash_merge_batch_size=HASH_MERGE
- Merge n adjacency lists at a time
- -k K, --kmer=K
- k-mer size used for hashing
- -e E, --min_error_tolerance=E
- Minimum error tolerance for parameter searching
- -E E, --max_error_tolerance=E
- Maximum error tolerance for parameter searching
- --hh=H, --min_minimum_overlap=H
- Minimum minimum overlap length for parameter searching
- --hH=H, --max_minimum_overlap=H
- Maximum minimum overlap length for parameter searching
- --h_rate=H_RATE, --heterozygous_rate=H_RATE
- Rate for heterozygous site
- --model_selection_size=MSIZE
- Model selection data set size
- --keep_all_files
- Keep all temporary files. By default, temporary files are deleted automatically.
| April 2013 | uc-echo |