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1 calc_fastq-stats
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2 ================
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3
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4 `calc_fastq-stats.pl` is a script to calculate basic statistics for bases and reads in a FASTQ file.
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5
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6 * [Synopsis](#synopsis)
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7 * [Description](#description)
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8 * [Usage](#usage)
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9 * [Options](#options)
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10 * [Mandatory options](#mandatory-options)
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11 * [Optional options](#optional-options)
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12 * [Output](#output)
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13 * [Run environment](#run-environment)
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14 * [Dependencies](#dependencies)
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15 * [Author - contact](#author---contact)
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16 * [Citation, installation, and license](#citation-installation-and-license)
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17 * [Changelog](#changelog)
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18
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19 ## Synopsis
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20
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21 perl calc_fastq-stats.pl -i reads.fastq
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22
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23 **or**
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24
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25 gzip -dc reads.fastq.gz | perl calc_fastq-stats.pl -i -
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26
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27 ## Description
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28
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29 The script calculates some simple statistics, like individual and total base
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30 counts, GC content, and basic stats for the read lengths, and
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31 read/base qualities in a FASTQ file. The GC content calculation does
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32 not include 'N's. Stats are printed to *STDOUT* and optionally to an
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33 output file.
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34
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35 Because the quality of a read degrades over its length with all NGS
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36 machines, it is advisable to also plot the quality for each cycle as
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37 implemented in tools like
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38 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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39 or the [fastx-toolkit](http://hannonlab.cshl.edu/fastx_toolkit/).
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40
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41 If the sequence and the quality values are interrupted by line
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42 breaks (i.e. a read is **not** represented by four lines), please fix
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43 with Heng Li's [seqtk](https://github.com/lh3/seqtk):
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44
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45 seqtk seq -l 0 infile.fastq > outfile.fastq
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46
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47 An alternative tool, which is a lot faster, is **fastq-stats** from
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48 [ea-utils](https://code.google.com/p/ea-utils/).
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49
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50 ## Usage
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51
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52 zcat reads.fastq.gz | perl calc_fastq-stats.pl -i - -q 64 -c 175000000 -n 3000000
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53
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54 ## Options
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55
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56 ### Mandatory options
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57
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58 - -i, -input
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59
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60 Input FASTQ file or piped STDIN (-) from a gzipped file
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61
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62 - -q, -qual_offset
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63
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64 ASCII quality offset of the Phred (Sanger) quality values [default 33]
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65
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66 ### Optional options
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67
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68 - -h, -help:
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69
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70 Help (perldoc POD)
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71
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72 - -c, -coverage_limit
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73
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74 Number of bases to sample from the top of the file
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75
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76 - -n, -num_read
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77
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78 Number of reads to sample from the top of the file
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79
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80 - -o, -output
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81
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82 Print stats in addition to *STDOUT* to the specified output file
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83
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84 - -v, -version
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85
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86 Print version number to *STDERR*
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87
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88 ## Output
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89
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90 - *STDOUT*
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91
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92 Calculated stats are printed to *STDOUT*
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93
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94 - (outfile)
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95
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96 Optional outfile for stats
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97
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98 ## Run environment
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99
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100 The Perl script runs under Windows and UNIX flavors.
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101
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102 ## Dependencies
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103
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104 If the following modules are not installed get them from
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105 [CPAN](http://www.cpan.org/):
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106
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107 - `Statistics::Descriptive`
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108
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109 Perl module to calculate basic descriptive statistics
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110
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111 - `Statistics::Descriptive::Discrete`
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112
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113 Perl module to calculate descriptive statistics for discrete data sets
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114
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115 - `Statistics::Descriptive::Weighted`
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116
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117 Perl module to calculate descriptive statistics for weighted variates
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118
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119 ## Author - contact
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120
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121 Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)
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122
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123 ## Citation, installation, and license
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124
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125 For [citation](https://github.com/aleimba/bac-genomics-scripts#citation), [installation](https://github.com/aleimba/bac-genomics-scripts#installation-recommendations), and [license](https://github.com/aleimba/bac-genomics-scripts#license) information please see the repository main [*README.md*](https://github.com/aleimba/bac-genomics-scripts/blob/master/README.md).
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126
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127 ## Changelog
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128
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129 - v0.1 (28.10.2014)
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