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
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH FAST5_TO_SEQ_SUMMARY "1" "December 2020" "Fast5_to_seq_summary 2.5.2" "User Commands"
.SH NAME
Fast5_to_seq_summary \- generate a sequencing summary like file from a directory containing Fast5 files
.SH DESCRIPTION
usage: Fast5_to_seq_summary [\-h] [\-\-version] \fB\-\-fast5_dir\fR FAST5_DIR
.TP
\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN
[\-\-max_fast5 MAX_FAST5] [\-\-threads THREADS]
[\-\-basecall_id BASECALL_ID]
[\-\-fields FIELDS [FIELDS ...]] [\-\-include_path]
[\-\-verbose_level VERBOSE_LEVEL]
.PP
Fast5_to_seq_summary generate a sequencing summary like file from a directory
containing Fast5 files
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR, \fB\-v\fR
show program's version number and exit
.TP
\fB\-\-fast5_dir\fR FAST5_DIR, \fB\-f\fR FAST5_DIR
Directory containing fast5 files. Can contain multiple
subdirectories
.TP
\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN, \fB\-s\fR SEQ_SUMMARY_FN
path of the summary sequencing file where to write the
data extracted from the fast5 files
.TP
\fB\-\-max_fast5\fR MAX_FAST5
Maximum number of file to try to parse. 0 to
deactivate (default: 0)
.TP
\fB\-\-threads\fR THREADS, \fB\-t\fR THREADS
Total number of threads to use. 1 thread is used for
the reader and 1 for the writer. Minimum 3 (default:
4)
.TP
\fB\-\-basecall_id\fR BASECALL_ID
id of the basecalling group. By default leave to 0,
but if you perfome multiple basecalling on the same
fast5 files, this can be used to indicate the
corresponding group (1, 2 ...) (default: 0)
.TP
\fB\-\-fields\fR FIELDS [FIELDS ...]
list of field names corresponding to attributes to try
to fetch from the fast5 files (default: ['read_id',
\&'run_id', 'channel', 'start_time',
\&'sequence_length_template', 'mean_qscore_template',
\&'calibration_strand_genome_template',
\&'barcode_arrangement'])
.TP
\fB\-\-include_path\fR
If given, the absolute path to the corresponding file
is added in an extra column (default: False)
.TP
\fB\-\-verbose_level\fR VERBOSE_LEVEL
Level of verbosity, from 2 (Chatty) to 0 (Nothing)
(default: 0)
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
|
