uc-echo(1) 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.