From b5ec9e8d92314c5111623c48528f9f54cc09d5de Mon Sep 17 00:00:00 2001 From: wdecoster Date: Sat, 30 May 2020 22:46:57 +0200 Subject: [PATCH] i don't know why but there is a readme.rst --- README.rst | 66 ++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 44 insertions(+), 22 deletions(-) diff --git a/README.rst b/README.rst index de63961..e1e50e5 100644 --- a/README.rst +++ b/README.rst @@ -3,11 +3,12 @@ Nanofilt Filtering and trimming of long read sequencing data. -|Twitter URL| |conda badge| |Build Status| |Code Health| +|Twitter URL| |conda badge| |Build Status| | Filtering on quality and/or read length, and optional trimming after passing filters. -| Reads from stdin, writes to stdout. +| Reads from stdin, writes to stdout. Optionally reads directly from an + uncompressed file specified on the command line. | Intended to be used: | - directly after fastq extraction @@ -21,8 +22,8 @@ Filtering and trimming of long read sequencing data. 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. + sequencing_summary.txt file from albacore will do the filtering using + the quality scores from the summary. It’s also faster. INSTALLATION AND UPGRADING: ~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -41,28 +42,45 @@ USAGE: :: - 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. + NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH] + [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC] + [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP] + [-s SUMMARY] [--readtype {1D,2D,1D2}] + [input] + + Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin. + + General options: + -h, --help show the help and exit + -v, --version Print version and exit. + --logfile LOGFILE Specify the path and filename for the log file. + input input, uncompressed fastq file (optional) + + Options for filtering reads on.: + -l, --length LENGTH Filter on a minimum read length + --maxlength MAXLENGTH Filter on a maximum read length + -q, --quality QUALITY Filter on a minimum average read quality score + --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. + + Options for trimming reads.: + --headcrop HEADCROP Trim n nucleotides from start of read + --tailcrop TAILCROP Trim n nucleotides from end of read + + Input options.: + -s, --summary SUMMARY Use albacore or guppy summary file for quality scores + --readtype Which read type to extract information about from summary. Options are 1D, 2D or 1D2 EXAMPLES ~~~~~~~~ .. 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 + 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 I welcome all suggestions, bug reports, feature requests and contributions. Please leave an @@ -70,11 +88,15 @@ contributions. Please leave an request. I will usually respond within a day, or rarely within a few days. +CITATION +-------- + +If you use this tool, please consider citing our +`publication `__. + .. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster :target: https://twitter.com/wouter_decoster .. |conda badge| image:: https://anaconda.org/bioconda/nanofilt/badges/installer/conda.svg :target: https://anaconda.org/bioconda/nanofilt .. |Build Status| image:: https://travis-ci.org/wdecoster/nanofilt.svg?branch=master :target: https://travis-ci.org/wdecoster/nanofilt -.. |Code Health| image:: https://landscape.io/github/wdecoster/nanofilt/master/landscape.svg?style=flat - :target: https://landscape.io/github/wdecoster/nanofilt/master