NanoFilt 1.9.2

Filtering and trimming of Oxford Nanopore Sequencing data

Nanofilt
========

Filtering and trimming of Oxford Nanopore sequencing data.

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| Filtering on quality and/or read length, and optional trimming after
passing filters.
| Reads from stdin, writes to stdout.

| Intended to be used:
| - directly after fastq extraction
| - prior to mapping
| - in a stream between extraction and mapping

| See also
``my post about NanoFilt on my blog Gigabase or gigabyte <https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/>`` \_\_.
| Due to
``a discrepancy <https://gigabaseorgigabyte.wordpress.com/2017/07/14/calculated-average-quality-vs-albacore-summary/>`` \_\_
between calculated read quality and the quality as summarized by
albacore this script takes since v1.1.0 optionally also a
``--summary`` argument. Using this argument with the
sequencing\_summary.txt file from albacore will do the filtering using
the quality scores from the summary. It's also faster.

INSTALLATION AND UPGRADING:
:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``~```````````\ ~\ :sub:``\ ~\`

.. code:: bash

::

::

pip install nanofilt
pip install nanofilt --upgrade

or

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.. code:: bash

::

::

conda install -c bioconda nanofilt

STATUS
------

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NanoFilt is written for Python 3.

USAGE: :sub:``:sub:``\ :sub:`\`\` `

::

::

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NanoFilt [-h] [-q QUALITY] [-l LENGTH] [--headcrop HEADCROP] [--tailcrop TAILCROP]

optional arguments:
-h, --help show this help message and exit
-s --summary SUMMARYFILE optional, the sequencing_summary file from albacore for extracting quality scores
-q, --quality QUALITY Filter on a minimum average read quality score
-l, --length LENGTH Filter on a minimum read length
--headcrop HEADCROP Trim n nucleotides from start of read
--tailcrop TAILCROP Trim n nucleotides from end of read
--minGC MINGC Sequences must have GC content >= to this. Float
between 0.0 and 1.0. Ignored if using summary file.
--maxGC MAXGC Sequences must have GC content <= to this. Float
between 0.0 and 1.0. Ignored if using summary file.

Example:

.. code:: bash

::

::

gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -
gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz
gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz

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