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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.


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.
  -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:    408254
Total bases:    3508315665
Median read length: 5168.0
Mean read length:   8593.46
Readlength N50: 39346

Top 5 read lengths and their average basecall quality score:
Length: 255821bp    Q: 6.84
Length: 254573bp    Q: 7.09
Length: 253711bp    Q: 6.96
Length: 245784bp    Q: 6.98
Length: 245776bp    Q: 7.06

Top 5 average basecall quality scores and their read lengths:
Length: 407bp   Q: 16.22
Length: 880bp   Q: 16.18
Length: 729bp   Q: 16.12
Length: 1057bp  Q: 16.08
Length: 841bp   Q: 15.84

Number of reads and fraction above quality cutoffs:
Q5: 406428  99.55%
Q10:    305509  74.83%
Q15:    124 0.03%
Q20:    0   0.0%

Project details


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NanoStat-0.3.0.tar.gz (3.6 kB view hashes)

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