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author rnateam
date Thu, 12 Nov 2015 08:56:59 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="flexbar" version="2.5">
4 <install version="1.0">
5 <actions_group>
6 <actions os="linux" architecture="x86_64">
7 <action type="download_by_url" target_filename="flexbar_v2.5_linux64.tgz">https://github.com/seqan/flexbar/releases/download/v2.5.0/flexbar_v2.5_linux64.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
15 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
16 </action>
17 </actions_group>
18 </install>
19 <readme>
20 flexbar - flexible barcode and adapter removal
21 ==============================================
22
23 SYNOPSIS
24 flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]
25
26 DESCRIPTION
27 -h, --help
28 Displays this help message.
29 -H, --advanced
30 Print help with advanced options.
31 -i, --cite
32 Show program reference for citation.
33
34 Basic options:
35 -n, --threads NUM
36 Number of threads to employ. Default: 1.
37 -t, --target STR
38 Prefix for output file names or paths. Default: flexbar.
39 -r, --reads FILE
40 Fasta/q file or stdin (-) with reads that may contain barcodes.
41 -p, --reads2 FILE
42 Second input file of paired reads, gz and bz2 files supported.
43 -f, --format STR
44 Quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+).
45 -c, --color-space
46 Input in color-space format csfasta or csfastq in sanger scaling.
47
48 Barcode detection:
49 -b, --barcodes FILE
50 Fasta file with barcodes for demultiplexing, may contain N.
51 -br, --barcode-reads FILE
52 Fasta/q file containing separate barcode reads for detection.
53 -be, --barcode-trim-end STR
54 Type of detection, see section trim-end modes. Default: ANY.
55 -bo, --barcode-min-overlap NUM
56 Minimum overlap of barcode and read. Default: barcode length.
57 -bt, --barcode-threshold NUM
58 Allowed mismatches and gaps per overlap of 10. Default: 1.0.
59 -bu, --barcode-unassigned
60 Include unassigned reads in output generation.
61
62 Adapter removal:
63 -a, --adapters FILE
64 Fasta file with adapters for removal that may contain N.
65 -as, --adapter-seq STR
66 Single adapter sequence as alternative to adapters option.
67 -ae, --adapter-trim-end STR
68 Type of removal, see section trim-end modes. Default: RIGHT.
69 -ao, --adapter-min-overlap NUM
70 Minimum overlap of adapter and read for removal. Default: 3.
71 -at, --adapter-threshold NUM
72 Allowed mismatches and gaps per overlap of 10. Default: 3.0.
73
74 Filtering and trimming:
75 -u, --max-uncalled NUM
76 Allowed uncalled bases (N or .) for each read. Default: 0.
77 -x, --pre-trim-left NUM
78 Trim given number of bases on 5' read end before detection.
79 -y, --pre-trim-right NUM
80 Trim specified number of bases on 3' end prior to detection.
81 -q, --pre-trim-phred NUM
82 Trim 3' end until specified or higher quality reached.
83 -k, --post-trim-length NUM
84 Trim to specified read length from 3' end after removal.
85 -m, --min-read-length NUM
86 Minimum read length to remain after removal. Default: 18.
87
88 Output selection:
89 -o, --fasta-output
90 Prefer non-quality format fasta or csfasta for output.
91 -z, --zip-output STR
92 Direct compression of output files. One of GZ and BZ2.
93 -s, --single-reads
94 Write single paired reads for too short counterparts.
95
96 Logging and tagging:
97 -l, --log-level STR
98 Print chosen read alignments. One of ALL, MOD, and TAB.
99 -g, --removal-tags
100 Tag reads that are subject to adapter or barcode removal.
101
102 Trim-end modes:
103 ANY: longer side of read remains after removal of overlap
104 LEFT: right side remains after removal, align &lt;= read end
105 RIGHT: left part remains after removal, align &gt;= read start
106 LEFT_TAIL: consider first n bases of reads in alignment
107 RIGHT_TAIL: use only last n bases, see tail-length options
108
109 EXAMPLES
110 flexbar -r reads.fq -f i1.8 -t target -b brc.fa -a adap.fa
111 flexbar -r reads.csfastq.gz -a adap.fa -ao 5 -ae LEFT -c
112
113 VERSION
114 flexbar version: 2.5
115 Last update June 30, 2014
116
117 Advanced options: flexbar -H
118 </readme>
119 </package>
120 </tool_dependency>