1samtools-fqidx(1)            Bioinformatics tools            samtools-fqidx(1)
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NAME

6       samtools fqidx - Indexes or queries regions from a fastq file
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SYNOPSIS

9       samtools fqidx ref.fastq [region1 [...]]
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DESCRIPTION

13       Index  reference  sequence  in  the FASTQ format or extract subsequence
14       from indexed reference sequence. If no region is specified, fqidx  will
15       index  the  file and create <ref.fastq>.fai on the disk. If regions are
16       specified, the subsequences will be retrieved and printed to stdout  in
17       the FASTQ format.
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19       The input file can be compressed in the BGZF format.
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21       The  sequences  in  the input file should all have different names.  If
22       they do not, indexing will emit a warning about duplicate sequences and
23       retrieval  will  only produce subsequences from the first sequence with
24       the duplicated name.
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26       samtools fqidx should only be used on fastq files with a  small  number
27       of  entries.   Trying  to use it on a file containing millions of short
28       sequencing reads will produce an index that is almost  as  big  as  the
29       original file, and searches using the index will be very slow and use a
30       lot of memory.
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OPTIONS

34       -o, --output FILE
35               Write FASTQ to file rather than to stdout.
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37       -n, --length INT
38               Length of FASTQ sequence line.  [60]
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40       -c, --continue
41               Continue working if a non-existent region is requested.
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43       -r, --region-file FILE
44               Read regions from a file. Format is chr:from-to, one per line.
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46       -i, --reverse-complement
47               Output the sequence as the reverse complement.  When  this  op‐
48               tion is used, “/rc” will be appended to the sequence names.  To
49               turn this off or change the string appended,  use  the  --mark-
50               strand option.
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52       --mark-strand TYPE
53               Append strand indicator to sequence name.  TYPE can be one of:
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55               rc     Append  '/rc' when writing the reverse complement.  This
56                      is the default.
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58               no     Do not append anything.
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60               sign   Append '(+)' for forward strand  or  '(-)'  for  reverse
61                      complement.   This  matches the output of “bedtools get‐
62                      fasta -s”.
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64               custom,<pos>,<neg>
65                      Append string <pos> to names when  writing  the  forward
66                      strand  and <neg> when writing the reverse strand.  Spa‐
67                      ces are preserved, so it is possible to move the indica‐
68                      tor into the comment part of the description line by in‐
69                      cluding a leading space in the strings <pos> and <neg>.
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71       --fai-idx FILE
72               Read/Write to specified index file.
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74       --gzi-idx FILE
75               Read/Write to specified compressed file index  (used  with  .gz
76               files).
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78       -h, --help
79               Print help message and exit.
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AUTHOR

83       Written  by  Heng  Li, with modifications by Andrew Whitwham and Robert
84       Davies, all from the Sanger Institute.
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SEE ALSO

88       samtools(1), samtools-faidx(1), samtools-fasta(1), samtools-fastq(1)
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90       Samtools website: <http://www.htslib.org/>
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94samtools-1.13                     7 July 2021                samtools-fqidx(1)