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1 '\" t
2 .TH faidx 5 "August 2013" "htslib" "Bioinformatics formats"
3 .SH NAME
4 faidx \- an index enabling random access to FASTA files
5 .\"
6 .\" Copyright (C) 2013 Genome Research Ltd.
7 .\"
8 .\" Author: John Marshall <jm18@sanger.ac.uk>
9 .\"
10 .\" Permission is hereby granted, free of charge, to any person obtaining a
11 .\" copy of this software and associated documentation files (the "Software"),
12 .\" to deal in the Software without restriction, including without limitation
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15 .\" Software is furnished to do so, subject to the following conditions:
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17 .\" The above copyright notice and this permission notice shall be included in
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20 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
21 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
22 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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27 .\"
28 .SH SYNOPSIS
29 .IR file.fa .fai,
30 .IR file.fasta .fai
31 .SH DESCRIPTION
32 Using an \fBfai index\fP file in conjunction with a FASTA file containing
33 reference sequences enables efficient access to arbitrary regions within
34 those reference sequences.
35 The index file typically has the same filename as the corresponding FASTA
36 file, with \fB.fai\fP appended.
37 .P
38 An \fBfai index\fP file is a text file consisting of lines each with
39 five TAB-delimited columns:
40 .TS
41 lbl.
42 NAME Name of this reference sequence
43 LENGTH Total length of this reference sequence, in bases
44 OFFSET Offset within the FASTA file of this sequence's first base
45 LINEBASES The number of bases on each line
46 LINEWIDTH The number of bytes in each line, including the newline
47 .TE
48 .P
49 The \fBNAME\fP and \fBLENGTH\fP columns contain the same
50 data as would appear in the \fBSN\fP and \fBLN\fP fields of a
51 SAM \fB@SQ\fP header for the same reference sequence.
52 .P
53 The \fBOFFSET\fP column contains the offset within the FASTA file, in bytes
54 starting from zero, of the first base of this reference sequence, i.e., of
55 the character following the newline at the end of the "\fB>\fP" header line.
56 Typically the lines of a \fBfai index\fP file appear in the order in which the
57 reference sequences appear in the FASTA file, so \fB.fai\fP files are typically
58 sorted according to this column.
59 .P
60 The \fBLINEBASES\fP column contains the number of bases in each of the sequence
61 lines that form the body of this reference sequence, apart from the final line
62 which may be shorter.
63 The \fBLINEWIDTH\fP column contains the number of \fIbytes\fP in each of
64 the sequence lines (except perhaps the final line), thus differing from
65 \fBLINEBASES\fP in that it also counts the bytes forming the line terminator.
66 .SS FASTA Files
67 In order to be indexed with \fBsamtools faidx\fP, a FASTA file must be a text
68 file of the form
69 .LP
70 .RS
71 .RI > name
72 .RI [ description ...]
73 .br
74 ATGCATGCATGCATGCATGCATGCATGCAT
75 .br
76 GCATGCATGCATGCATGCATGCATGCATGC
77 .br
78 ATGCAT
79 .br
80 .RI > name
81 .RI [ description ...]
82 .br
83 ATGCATGCATGCAT
84 .br
85 GCATGCATGCATGC
86 .br
87 [...]
88 .RE
89 .LP
90 In particular, each reference sequence must be "well-formatted", i.e., all
91 of its sequence lines must be the same length, apart from the final sequence
92 line which may be shorter.
93 (While this sequence line length must be the same within each sequence,
94 it may vary between different reference sequences in the same FASTA file.)
95 .P
96 This also means that although the FASTA file may have Unix- or Windows-style
97 or other line termination, the newline characters present must be consistent,
98 at least within each reference sequence.
99 .P
100 The \fBsamtools\fP implementation uses the first word of the "\fB>\fP" header
101 line text (i.e., up to the first whitespace character) as the \fBNAME\fP column.
102 At present, there may be no whitespace between the
103 ">" character and the \fIname\fP.
104 .SH EXAMPLE
105 For example, given this FASTA file
106 .LP
107 .RS
108 >one
109 .br
110 ATGCATGCATGCATGCATGCATGCATGCAT
111 .br
112 GCATGCATGCATGCATGCATGCATGCATGC
113 .br
114 ATGCAT
115 .br
116 >two another chromosome
117 .br
118 ATGCATGCATGCAT
119 .br
120 GCATGCATGCATGC
121 .br
122 .RE
123 .LP
124 formatted with Unix-style (LF) line termination, the corresponding fai index
125 would be
126 .RS
127 .TS
128 lnnnn.
129 one 66 5 30 31
130 two 28 98 14 15
131 .TE
132 .RE
133 .LP
134 If the FASTA file were formatted with Windows-style (CR-LF) line termination,
135 the fai index would be
136 .RS
137 .TS
138 lnnnn.
139 one 66 6 30 32
140 two 28 103 14 16
141 .TE
142 .RE
143 .SH SEE ALSO
144 .IR samtools (1)
145 .TP
146 http://en.wikipedia.org/wiki/FASTA_format
147 Further description of the FASTA format