faidx(5) - f36

1faidx(5)                    Bioinformatics formats                    faidx(5)
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NAME

6       faidx - an index enabling random access to FASTA and FASTQ files
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SYNOPSIS

9       file.fa.fai, file.fasta.fai, file.fq.fai, file.fastq.fai
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DESCRIPTION

12       Using an fai index file in conjunction with a FASTA/FASTQ file contain‐
13       ing reference sequences enables efficient access to  arbitrary  regions
14       within  those  reference  sequences.   The index file typically has the
15       same  filename  as  the  corresponding  FASTA/FASTQ  file,  with   .fai
16       appended.
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18       An  fai  index  file  is a text file consisting of lines each with five
19       TAB-delimited columns for a FASTA file and six for FASTQ:
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21       NAME         Name of this reference sequence
22       LENGTH       Total length of this reference sequence, in bases
23       OFFSET       Offset in the FASTA/FASTQ file of this sequence's first base
24       LINEBASES    The number of bases on each line
25       LINEWIDTH    The number of bytes in each line, including the newline
26       QUALOFFSET   Offset of sequence's first quality within the FASTQ file
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28       The NAME and LENGTH columns contain the same data as  would  appear  in
29       the  SN  and  LN  fields  of  a  SAM  @SQ header for the same reference
30       sequence.
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32       The OFFSET column contains the offset within the FASTA/FASTQ  file,  in
33       bytes starting from zero, of the first base of this reference sequence,
34       i.e., of the character following the newline at the end of  the  header
35       line  (the  ">"  line in FASTA, "@" in FASTQ). Typically the lines of a
36       fai index file appear in the order in  which  the  reference  sequences
37       appear  in  the  FASTA/FASTQ  file,  so .fai files are typically sorted
38       according to this column.
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40       The LINEBASES column contains the  number  of  bases  in  each  of  the
41       sequence  lines  that  form  the body of this reference sequence, apart
42       from the final line which may be shorter.  The  LINEWIDTH  column  con‐
43       tains the number of bytes in each of the sequence lines (except perhaps
44       the final line), thus differing from LINEBASES in that it  also  counts
45       the bytes forming the line terminator.
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47       The  QUALOFFSET  works the same way as OFFSET but for the first quality
48       score of this reference sequence.  This would be  the  first  character
49       following  the  newline  at  the  end of the "+" line.  For FASTQ files
50       only.
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52   FASTA Files
53       In order to be indexed with samtools faidx, a FASTA file must be a text
54       file of the form
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56              >name [description...]
57              ATGCATGCATGCATGCATGCATGCATGCAT
58              GCATGCATGCATGCATGCATGCATGCATGC
59              ATGCAT
60              >name [description...]
61              ATGCATGCATGCAT
62              GCATGCATGCATGC
63              [...]
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65       In  particular, each reference sequence must be "well-formatted", i.e.,
66       all of its sequence lines must be the same length, apart from the final
67       sequence  line  which may be shorter.  (While this sequence line length
68       must be the same within each sequence, it may  vary  between  different
69       reference sequences in the same FASTA file.)
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71       This also means that although the FASTA file may have Unix- or Windows-
72       style or other line termination, the newline characters present must be
73       consistent, at least within each reference sequence.
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75       The  samtools implementation uses the first word of the ">" header line
76       text (i.e., up to the first whitespace character,  having  skipped  any
77       initial whitespace after the ">") as the NAME column.
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79   FASTQ Files
80       FASTQ files for indexing work in the same way as the FASTA files.
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82              @name [description...]
83              ATGCATGCATGCATGCATGCATGCATGCAT
84              GCATGCATGCATGCATGCATGCATGCATGC
85              ATGCAT
86              +
87              FFFA@@FFFFFFFFFFHHB:::@BFFFFGG
88              HIHIIIIIIIIIIIIIIIIIIIIIIIFFFF
89              8011<<
90              @name [description...]
91              ATGCATGCATGCAT
92              GCATGCATGCATGC
93              +
94              IIA94445EEII==
95              =>IIIIIIIIICCC
96              [...]
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98       Quality  lines  must be wrapped at the same length as the corresponding
99       sequence lines.
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EXAMPLE

102       For example, given this FASTA file
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104              >one
105              ATGCATGCATGCATGCATGCATGCATGCAT
106              GCATGCATGCATGCATGCATGCATGCATGC
107              ATGCAT
108              >two another chromosome
109              ATGCATGCATGCAT
110              GCATGCATGCATGC
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112       formatted with Unix-style (LF) line termination, the corresponding  fai
113       index would be
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115              one   66    5   30   31
116              two   28   98   14   15
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118       If the FASTA file were formatted with Windows-style (CR-LF) line termi‐
119       nation, the fai index would be
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121              one   66     6   30   32
122              two   28   103   14   16
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124       An example FASTQ file
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126              @fastq1
127              ATGCATGCATGCATGCATGCATGCATGCAT
128              GCATGCATGCATGCATGCATGCATGCATGC
129              ATGCAT
130              +
131              FFFA@@FFFFFFFFFFHHB:::@BFFFFGG
132              HIHIIIIIIIIIIIIIIIIIIIIIIIFFFF
133              8011<<
134              @fastq2
135              ATGCATGCATGCAT
136              GCATGCATGCATGC
137              +
138              IIA94445EEII==
139              =>IIIIIIIIICCC
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141       Formatted with Unix-style line termination would give this fai index
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143              fastq1   66     8   30   31    79
144              fastq2   28   156   14   15   188
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NAME

SYNOPSIS

DESCRIPTION

EXAMPLE

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