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Calculate statistics for Oxford Nanopore sequencing data and alignments

Project description

Calculate various statistics from an Oxford Nanopore dataset in fastq, bam or albacore sequencing summary format.

Twitter URL install with conda Build Status Code Health

INSTALLATION

pip install nanostat
or
install with conda
conda install -c bioconda nanostat

USAGE

NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-t THREADS]
                (--fastq FASTQ | --summary SUMMARY | --bam BAM)

Get statistics of Oxford Nanopore read dataset.

Mandatory one of the following data sources:
--fastq FASTQ         Data is in fastq format.
--summary SUMMARY     Data is a summary file generated by albacore.
--bam BAM             Data as a sorted bam file.
Specifying a list of files of the same type is supported.

Optional arguments:
  --readtype            Specify read type to extract from summary file
                        Options: 1D (default), 2D or 1D2
  -h, --help            show this help message and exit
  -v, --version         Print version and exit.
  -o, --outdir OUTDIR   Specify directory in which output has to be created.
  -n, --name NAME       Specify a custom filename/path for the output,
                        <stdout> for printing to stdout.
  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
  -t, --threads THREADS Set the allowed number of threads to be used by the script
                        This only applies to bam and fastq format as data source

STATUS

Build Status Code Health

Example output

Number of reads:        99875
Total bases:    779100562
Median read length:     5456.0
Mean read length:       7800.76
Readlength N50: 12658

Top 5 read lengths and their average basecall quality score:
Length: 299625bp        Q: 10.36
Length: 272879bp        Q: 9.99
Length: 271441bp        Q: 10.94
Length: 261038bp        Q: 8.0
Length: 250267bp        Q: 7.74

Top 5 average basecall quality scores and their read lengths:
Length: 1455bp  Q: 16.54
Length: 3634bp  Q: 16.48
Length: 733bp   Q: 16.23
Length: 515bp   Q: 16.2
Length: 909bp   Q: 15.89

Number of reads and fraction above quality cutoffs:
Q5:     88489   88.6%
Q10:    61809   61.89%
Q15:    175     0.18%
Q20:    0       0.0%

Data produced using 512 active channels.

Data was produced in run(s) with ID:
002dc25e406b22dd8e4d2a5ee83dcbb67072e10d
005aaa922c42c455c07a472a9c30f0209f1b0d93
00b31b64541f79ff1f562c3e3602d3f265cd3b05
00c9faabd00f4676a2255da178a62c1fe6ae061b
00f9dec9cb591f4cb4c60c129f87faf731323386

Project details


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Source Distribution

NanoStat-0.6.1.tar.gz (4.0 kB view hashes)

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