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Missing documentation of `-ins_length` in oases help message
I am running oases version 0.2.09
installed from bioconda. When I run oases --help
, then I get the usage message below, which includes documentation for -ins_length2
, but not for -ins_length
. This lack of documentation has caused substantial confusion to this user. Perhaps it might be worth including -ins_length
in the oases help message.
Usage:
./oases directory [options]
directory : working directory name
Standard options:
--help : this help message
--version : print version and exit
--citation : print citation to Oases manuscript and exit
-ins_length2 <integer> : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
-ins_length_long <integer> : expected distance between two long paired-end reads (default: no read pairing)
-ins_length*_sd <integer> : est. standard deviation of respective dataset (default: 10% of corresponding length)
[replace '*' by nothing, '2' or '_long' as necessary]
-unused_reads <yes|no> : export unused reads in UnusedReads.fa file (default: no)
-amos_file <yes|no> : export assembly to AMOS file (default: no export)
-alignments <yes|no> : export a summary of contig alignment to the reference sequences (default: no)
Advanced options:
-cov_cutoff <floating-point> : removal of low coverage nodes AFTER tour bus or allow the system to infer it (default: 3)
-min_pair_count <integer> : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 4)
-min_trans_lgth <integer> : Minimum length of output transcripts (default: hash-length)
-paired_cutoff <floating-point> : minimum ratio allowed between the numbers of observed and estimated connecting read pairs
Must be part of the open interval ]0,1[ (default: 0.1)
-merge <yes|no> :Preserve contigs mapping onto long sequences to be preserved from coverage cutoff (default: no)
-edgeFractionCutoff <floating-point> : Remove edges which represent less than that fraction of a nodes outgoing flow
Must be part of the open interval ]0,1[ (default: 0.01)
-scaffolding <yes|no> : Allow gaps in transcripts (default: no)
-degree_cutoff <integer> : Maximum allowed degree on either end of a contigg to consider it 'unique' (default: 3)
Output:
directory/transcripts.fa
directory/contig-ordering.txt