.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH UC-ECHO "1" "April 2013" "uc-echo" "User Commands"
.SH NAME
uc-echo -  Short-read Error Correction
.SH SYNOPSIS
.B uc-echo 
[\fIoptions\fR] \fIread_file_name\fR
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUTPUT_FILENAME, \fB\-\-output\fR=\fIOUTPUT_FILENAME\fR
Output file name
.TP
\fB\-l\fR LOG_FILENAME, \fB\-\-log\fR=\fILOG_FILENAME\fR
Log file name
.TP
\fB\-\-DD\fR=\fITMP_DIRECTORY\fR, \fB\-\-tmp_dir\fR=\fITMP_DIRECTORY\fR
Temporary data directory
.TP
\fB\-u\fR NCPU, \fB\-\-ncpu\fR=\fINCPU\fR
Number of processes used in training
.TP
\fB\-b\fR BSIZE, \fB\-\-block_size\fR=\fIBSIZE\fR
Split data into blocks of specified size
.TP
\fB\-\-nh\fR=\fINHASH\fR, \fB\-\-n_hash_block\fR=\fINHASH\fR
Split hash table into n tables
.TP
\fB\-\-rm\fR=\fIREAD_MERGE\fR, \fB\-\-read_merge_size\fR=\fIREAD_MERGE\fR
Merge n hash tables at a time
.TP
\fB\-\-hm\fR=\fIHASH_MERGE\fR, \fB\-\-hash_merge_batch_size\fR=\fIHASH_MERGE\fR
Merge n adjacency lists at a time
.TP
\fB\-k\fR K, \fB\-\-kmer\fR=\fIK\fR
k\-mer size used for hashing
.TP
\fB\-e\fR E, \fB\-\-min_error_tolerance\fR=\fIE\fR
Minimum error tolerance for parameter searching
.TP
\fB\-E\fR E, \fB\-\-max_error_tolerance\fR=\fIE\fR
Maximum error tolerance for parameter searching
.TP
\fB\-\-hh\fR=\fIH\fR, \fB\-\-min_minimum_overlap\fR=\fIH\fR
Minimum minimum overlap length for parameter searching
.TP
\fB\-\-hH\fR=\fIH\fR, \fB\-\-max_minimum_overlap\fR=\fIH\fR
Maximum minimum overlap length for parameter searching
.TP
\fB\-\-h_rate\fR=\fIH_RATE\fR, \fB\-\-heterozygous_rate\fR=\fIH_RATE\fR
Rate for heterozygous site
.TP
\fB\-\-model_selection_size\fR=\fIMSIZE\fR
Model selection data set size
.TP
\fB\-\-keep_all_files\fR
Keep all temporary files. By default, temporary files
are deleted automatically.
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUTPUT_FILENAME, \fB\-\-output\fR=\fIOUTPUT_FILENAME\fR
Output file name
.TP
\fB\-l\fR LOG_FILENAME, \fB\-\-log\fR=\fILOG_FILENAME\fR
Log file name
.TP
\fB\-\-DD\fR=\fITMP_DIRECTORY\fR, \fB\-\-tmp_dir\fR=\fITMP_DIRECTORY\fR
Temporary data directory
.TP
\fB\-u\fR NCPU, \fB\-\-ncpu\fR=\fINCPU\fR
Number of processes used in training
.TP
\fB\-b\fR BSIZE, \fB\-\-block_size\fR=\fIBSIZE\fR
Split data into blocks of specified size
.TP
\fB\-\-nh\fR=\fINHASH\fR, \fB\-\-n_hash_block\fR=\fINHASH\fR
Split hash table into n tables
.TP
\fB\-\-rm\fR=\fIREAD_MERGE\fR, \fB\-\-read_merge_size\fR=\fIREAD_MERGE\fR
Merge n hash tables at a time
.TP
\fB\-\-hm\fR=\fIHASH_MERGE\fR, \fB\-\-hash_merge_batch_size\fR=\fIHASH_MERGE\fR
Merge n adjacency lists at a time
.TP
\fB\-k\fR K, \fB\-\-kmer\fR=\fIK\fR
k\-mer size used for hashing
.TP
\fB\-e\fR E, \fB\-\-min_error_tolerance\fR=\fIE\fR
Minimum error tolerance for parameter searching
.TP
\fB\-E\fR E, \fB\-\-max_error_tolerance\fR=\fIE\fR
Maximum error tolerance for parameter searching
.TP
\fB\-\-hh\fR=\fIH\fR, \fB\-\-min_minimum_overlap\fR=\fIH\fR
Minimum minimum overlap length for parameter searching
.TP
\fB\-\-hH\fR=\fIH\fR, \fB\-\-max_minimum_overlap\fR=\fIH\fR
Maximum minimum overlap length for parameter searching
.TP
\fB\-\-h_rate\fR=\fIH_RATE\fR, \fB\-\-heterozygous_rate\fR=\fIH_RATE\fR
Rate for heterozygous site
.TP
\fB\-\-model_selection_size\fR=\fIMSIZE\fR
Model selection data set size
.TP
\fB\-\-keep_all_files\fR
Keep all temporary files. By default, temporary files
are deleted automatically.