i don't know why but there is a readme.rst

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:
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -41,40 +42,61 @@ 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
 `issue <https://github.com/wdecoster/nanofilt/issues>`__ or open a pull
 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 <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
+
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    :target: https://travis-ci.org/wdecoster/nanofilt
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-   :target: https://landscape.io/github/wdecoster/nanofilt/master