debian/changelog

+unicycler (0.4.7+dfsg-2) UNRELEASED; urgency=medium
+
+  * Add manpages
+
+ -- Andreas Tille <tille@debian.org>  Wed, 24 Oct 2018 09:04:28 +0200
+
 unicycler (0.4.7+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #908599)

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr  \
+         --name="assembly pipeline for bacterial genomes" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=unicycler_align
+help2man --no-info --no-discard-stderr  \
+         --name="sensitive semi-global long read aligner" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+
+progname=unicycler_check
+help2man --no-info --no-discard-stderr  \
+         --name="long read assembly checker" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=unicycler_polish
+help2man --no-info --no-discard-stderr  \
+         --name="Unicycler polish - hybrid assembly polishing" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=unicycler_scrub
+help2man --no-info --no-discard-stderr  \
+         --name="read trimming, chimera detection and misassembly detection" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/manpages

+debian/mans/*.1

debian/mans/unicycler.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UNICYCLER "1" "October 2018" "unicycler 0.4.7" "User Commands"
+.SH NAME
+unicycler \- assembly pipeline for bacterial genomes
+.SH SYNOPSIS
+.B unicycler
+[\-h] [\-\-help_all] [\-\-version] [\-1 SHORT1] [\-2 SHORT2]
+[\-s UNPAIRED] [\-l LONG] \fB\-o\fR OUT [\-\-verbosity VERBOSITY]
+[\-\-min_fasta_length MIN_FASTA_LENGTH] [\-\-keep KEEP]
+[\-t THREADS] [\-\-mode {conservative,normal,bold}]
+[\-\-linear_seqs LINEAR_SEQS] [\-\-vcf]
+.SH DESCRIPTION
+Unicycler is an assembly pipeline for bacterial genomes. It can assemble
+Illumina-only read sets where it functions as a SPAdes-optimiser. It can
+also assembly long-read-only sets (PacBio or Nanopore) where it runs a
+miniasm+Racon pipeline. For the best possible assemblies, give it both
+Illumina reads and long reads, and it will conduct a hybrid assembly.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this help message and exit
+.TP
+\fB\-\-help_all\fR
+Show a help message with all program options
+.TP
+\fB\-\-version\fR
+Show Unicycler's version number
+.SS Input
+.TP
+\fB\-1\fR SHORT1, \fB\-\-short1\fR SHORT1
+FASTQ file of first short reads in each pair
+(required)
+.TP
+\fB\-2\fR SHORT2, \fB\-\-short2\fR SHORT2
+FASTQ file of second short reads in each pair
+(required)
+.TP
+\fB\-s\fR UNPAIRED, \fB\-\-unpaired\fR UNPAIRED
+FASTQ file of unpaired short reads (optional)
+.TP
+\fB\-l\fR LONG, \fB\-\-long\fR LONG
+FASTQ or FASTA file of long reads (optional)
+.SS Output
+.TP
+\fB\-o\fR OUT, \fB\-\-out\fR OUT
+Output directory (required)
+.TP
+\fB\-\-verbosity\fR VERBOSITY
+Level of stdout and log file information (default: 1)
+.IP
+0 = no stdout,
+.IP
+1 = basic progress indicators,
+.IP
+2 = extra info,
+.IP
+3 = debugging info
+.TP
+\fB\-\-min_fasta_length\fR MIN_FASTA_LENGTH
+Exclude contigs from the FASTA file which are
+shorter than this length (default: 100)
+.TP
+\fB\-\-keep\fR KEEP
+Level of file retention (default: 1)
+.IP
+0 = only keep final files: assembly (FASTA,GFA and log),
+.IP
+1 = also save graphs at main checkpoints,
+.IP
+2 = also keep SAM (enables fast rerun in different mode),
+.IP
+3 = keep all temp files and save all graphs (for debugging)
+.TP
+\fB\-\-vcf\fR
+Produce a VCF by mapping the short reads to the
+final assembly (experimental, default: do not
+produce a vcf file)
+.SS Other
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of threads used (default: 4)
+.TP
+\fB\-\-mode\fR {conservative,normal,bold}
+Bridging mode (default: normal)
+.IP
+conservative = smaller contigs, lowest misassembly rate
+.IP
+normal = moderate contig size and misassembly rate
+.IP
+bold = longest contigs, higher misassembly rate
+.TP
+\fB\-\-linear_seqs\fR LINEAR_SEQS
+The expected number of linear (i.e. non\-circular)
+sequences in the underlying sequence (default: 0)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/unicycler_align.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UNICYCLER_ALIGN "1" "October 2018" "unicycler_align 0.4.7" "User Commands"
+.SH NAME
+unicycler_align \- sensitive semi-global long read aligner
+.SH SYNOPSIS
+.B unicycler_align
+[\-h] \fB\-\-ref\fR REF \fB\-\-reads\fR READS \fB\-\-sam\fR SAM
+[\-\-contamination CONTAMINATION] [\-\-scores SCORES]
+[\-\-low_score LOW_SCORE] [\-\-keep_bad]
+[\-\-sensitivity SENSITIVITY] [\-\-threads THREADS]
+[\-\-verbosity VERBOSITY] [\-\-min_len MIN_LEN]
+[\-\-allowed_overlap ALLOWED_OVERLAP]
+.SH DESCRIPTION
+Unicycler align \- a sensitive semi\-global long read aligner
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-ref\fR REF
+FASTA file containing one or more reference
+sequences
+.TP
+\fB\-\-reads\fR READS
+FASTQ or FASTA file of long reads
+.TP
+\fB\-\-sam\fR SAM
+SAM file of resulting alignments
+.TP
+\fB\-\-contamination\fR CONTAMINATION
+FASTA file of known contamination in long reads
+.TP
+\fB\-\-scores\fR SCORES
+Comma\-delimited string of alignment scores: match,
+mismatch, gap open, gap extend (default: 3,\-6,\-5,\-2)
+.TP
+\fB\-\-low_score\fR LOW_SCORE
+Score threshold \- alignments below this are
+considered poor (default: set threshold
+automatically)
+.TP
+\fB\-\-keep_bad\fR
+Include alignments in the results even if they are
+below the low score threshold (default: low\-scoring
+alignments are discarded)
+.TP
+\fB\-\-sensitivity\fR SENSITIVITY
+A number from 0 (least sensitive) to 3 (most
+sensitive) (default: 0)
+.TP
+\fB\-\-threads\fR THREADS
+Number of threads used (default: number of CPUs, up
+to 8)
+.TP
+\fB\-\-verbosity\fR VERBOSITY
+Level of stdout information (0 to 4) (default: 1)
+.TP
+\fB\-\-min_len\fR MIN_LEN
+Minimum alignment length (bp) \- exclude alignments
+shorter than this length (default: 100)
+.TP
+\fB\-\-allowed_overlap\fR ALLOWED_OVERLAP
+Allow this much overlap between alignments in a
+single read (default: 100)
+.SH SEE ALSO
+unicycler(1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/unicycler_check.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UNICYCLER_CHECK "1" "October 2018" "unicycler_check 0.4.7" "User Commands"
+.SH NAME
+unicycler_check \- long read assembly checker
+.SH SYNOPSIS
+.B unicycler_check
+[\-h] \fB\-\-sam\fR SAM \fB\-\-ref\fR REF \fB\-\-reads\fR READS
+[\-\-min_len MIN_LEN]
+[\-\-error_window_size ERROR_WINDOW_SIZE]
+[\-\-depth_window_size DEPTH_WINDOW_SIZE]
+[\-\-error_rate_threshold ERROR_RATE_THRESHOLD]
+[\-\-depth_p_val DEPTH_P_VAL]
+[\-\-window_tables WINDOW_TABLES]
+[\-\-base_tables BASE_TABLES] [\-\-html HTML]
+[\-\-threads THREADS] [\-\-verbosity VERBOSITY]
+.SH DESCRIPTION
+Long read assembly checker
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-sam\fR SAM
+Input SAM file of alignments (if this file doesn't
+exist, the alignment will be performed with results
+saved to this file \- you can use the aligner
+arguments with this script)
+.TP
+\fB\-\-ref\fR REF
+FASTA file containing one or more reference
+sequences
+.TP
+\fB\-\-reads\fR READS
+FASTQ file of long reads
+.TP
+\fB\-\-min_len\fR MIN_LEN
+Minimum alignment length (bp) \- exclude alignments
+shorter than this length (default: 100)
+.TP
+\fB\-\-error_window_size\fR ERROR_WINDOW_SIZE
+Window size for error summaries (default: 100)
+.TP
+\fB\-\-depth_window_size\fR DEPTH_WINDOW_SIZE
+Window size for depth summaries (default: 100)
+.TP
+\fB\-\-error_rate_threshold\fR ERROR_RATE_THRESHOLD
+Threshold for high error rates, expressed as the
+fraction between the mean error rate and the random
+alignment error rate (default: 0.3)
+.TP
+\fB\-\-depth_p_val\fR DEPTH_P_VAL
+P\-value for low/high depth thresholds (default:
+0.001)
+.TP
+\fB\-\-window_tables\fR WINDOW_TABLES
+Path and/or prefix for table files summarising
+reference errors for reference windows (default: do
+not save window tables)
+.TP
+\fB\-\-base_tables\fR BASE_TABLES
+Path and/or prefix for table files summarising
+reference errors at each base (default: do not save
+base tables)
+.TP
+\fB\-\-html\fR HTML
+Path for HTML report (default: do not save HTML
+report)
+.TP
+\fB\-\-threads\fR THREADS
+Number of CPU threads used to align (default: the
+number of available CPUs)
+.TP
+\fB\-\-verbosity\fR VERBOSITY
+Level of stdout information (0 to 2) (default: 1)
+.SH SEE ALSO
+unicycler(1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/unicycler_polish.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UNICYCLER_POLISH "1" "October 2018" "unicycler_polish 0.4.7" "User Commands"
+.SH NAME
+unicycler_polish \- Unicycler polish - hybrid assembly polishing
+.SH SYNOPSIS
+.B unicycler_polish
+[\-h] \fB\-a\fR ASSEMBLY [\-1 SHORT1] [\-2 SHORT2]
+[\-\-pb_bax PB_BAX [PB_BAX ...]] [\-\-pb_bam PB_BAM]
+[\-\-pb_fasta PB_FASTA] [\-\-long_reads LONG_READS]
+[\-\-no_fix_local] [\-\-min_insert MIN_INSERT]
+[\-\-max_insert MAX_INSERT]
+[\-\-min_align_length MIN_ALIGN_LENGTH]
+[\-\-homopolymer HOMOPOLYMER] [\-\-large LARGE]
+[\-\-illumina_alt ILLUMINA_ALT]
+[\-\-freebayes_qual_cutoff FREEBAYES_QUAL_CUTOFF]
+[\-\-threads THREADS] [\-\-verbosity VERBOSITY]
+[\-\-samtools SAMTOOLS] [\-\-bowtie2 BOWTIE2]
+[\-\-minimap2 MINIMAP2] [\-\-freebayes FREEBAYES]
+[\-\-pitchfork PITCHFORK] [\-\-bax2bam BAX2BAM]
+[\-\-pbalign PBALIGN] [\-\-arrow ARROW] [\-\-pilon PILON]
+[\-\-java JAVA] [\-\-ale ALE] [\-\-racon RACON]
+[\-\-minimap MINIMAP] [\-\-nucmer NUCMER]
+[\-\-showsnps SHOWSNPS]
+.SH DESCRIPTION
+Unicycler polish \- hybrid assembly polishing
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.SS Assembly
+.TP
+\fB\-a\fR ASSEMBLY, \fB\-\-assembly\fR ASSEMBLY
+Input assembly to be polished
+.SS Short reads
+.IP
+To polish with short reads (using Pilon), provide two FASTQ files of
+paired\-end reads
+.TP
+\fB\-1\fR SHORT1, \fB\-\-short1\fR SHORT1
+FASTQ file of short reads (first reads in each pair)
+.TP
+\fB\-2\fR SHORT2, \fB\-\-short2\fR SHORT2
+FASTQ file of short reads (second reads in each
+pair)
+.SS PacBio reads
+.IP
+To polish with PacBio reads (using Arrow), provide one of the following
+.TP
+\fB\-\-pb_bax\fR PB_BAX [PB_BAX ...]
+PacBio raw bax.h5 read files
+.TP
+\fB\-\-pb_bam\fR PB_BAM
+PacBio BAM read file
+.TP
+\fB\-\-pb_fasta\fR PB_FASTA
+FASTA file of PacBio reads
+.SS Generic long reads
+.IP
+To polish with generic long reads, provide the following
+.TP
+\fB\-\-long_reads\fR LONG_READS
+FASTQ/FASTA file of long reads
+.SS Polishing settings
+Various settings for polishing behaviour (defaults should work well in
+most cases)
+.TP
+\fB\-\-no_fix_local\fR
+do not fix local misassemblies (default: False)
+.TP
+\fB\-\-min_insert\fR MIN_INSERT
+minimum valid short read insert size (default: auto)
+.TP
+\fB\-\-max_insert\fR MAX_INSERT
+maximum valid short read insert size (default: auto)
+.TP
+\fB\-\-min_align_length\fR MIN_ALIGN_LENGTH
+Minimum long read alignment length (default: 1000)
+.TP
+\fB\-\-homopolymer\fR HOMOPOLYMER
+Long read polish changes to a homopolymer of this
+length or greater will be ignored (default: 4)
+.TP
+\fB\-\-large\fR LARGE
+Variants of this size or greater will be assess as
+large variants (default: 10)
+.TP
+\fB\-\-illumina_alt\fR ILLUMINA_ALT
+When assessing long read changes with short read
+alignments, a variant will only be applied if the
+alternative occurrences in the short read alignments
+exceed this percentage (default: 5)
+.TP
+\fB\-\-freebayes_qual_cutoff\fR FREEBAYES_QUAL_CUTOFF
+Reject Pilon substitutions from long reads if the
+FreeBayes quality is less than this value (default:
+10.0)
+.SS Other settings
+.TP
+\fB\-\-threads\fR THREADS
+CPU threads to use in alignment and consensus
+(default: number of CPUs)
+.TP
+\fB\-\-verbosity\fR VERBOSITY
+Level of stdout information (0 to 3, default: 2)
+0 = no stdout, 1 = basic progress indicators,
+2 = extra info, 3 = debugging info
+.SS Tool locations
+If these required tools are not available in your PATH variable, specify
+their location here (depending on which input reads are used, some of
+these tools may not be required)
+.TP
+\fB\-\-samtools\fR SAMTOOLS
+path to samtools executable (default: samtools)
+.TP
+\fB\-\-bowtie2\fR BOWTIE2
+path to bowtie2 executable (default: bowtie2)
+.TP
+\fB\-\-minimap2\fR MINIMAP2
+path to minimap2 executable (default: minimap2)
+.TP
+\fB\-\-freebayes\fR FREEBAYES
+path to freebayes executable (default: freebayes)
+.TP
+\fB\-\-pitchfork\fR PITCHFORK
+Path to Pitchfork installation of PacBio tools
+(should contain bin and lib directories) (default: )
+.TP
+\fB\-\-bax2bam\fR BAX2BAM
+path to bax2bam executable (default: bax2bam)
+.TP
+\fB\-\-pbalign\fR PBALIGN
+path to pbalign executable (default: pbalign)
+.TP
+\fB\-\-arrow\fR ARROW
+path to arrow executable (default: arrow)
+.TP
+\fB\-\-pilon\fR PILON
+path to pilon jar file (default: pilon*.jar)
+.TP
+\fB\-\-java\fR JAVA
+path to java executable (default: java)
+.TP
+\fB\-\-ale\fR ALE
+path to ALE executable (default: ALE)
+.TP
+\fB\-\-racon\fR RACON
+path to racon executable (default: racon)
+.TP
+\fB\-\-minimap\fR MINIMAP
+path to miniasm executable (default: minimap)
+.TP
+\fB\-\-nucmer\fR NUCMER
+path to nucmer executable (default: nucmer)
+.TP
+\fB\-\-showsnps\fR SHOWSNPS
+path to show\-snps executable (default: show\-snps)
+.SH SEE ALSO
+unicycler(1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/unicycler_scrub.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH UNICYCLER_SCRUB "1" "October 2018" "unicycler_scrub 0.4.7" "User Commands"
+.SH NAME
+unicycler_scrub \- read trimming, chimera detection and misassembly detection
+.SH SYNOPSIS
+.B unicycler_scrub
+[\-h] \fB\-i\fR INPUT \fB\-o\fR OUT [\-r READS] [\-\-trim TRIM]
+[\-\-split SPLIT] [\-\-min_split_size MIN_SPLIT_SIZE]
+[\-\-discard_chimeras] [\-t THREADS] [\-\-keep_paf]
+[\-\-parameters PARAMETERS] [\-\-verbosity VERBOSITY]
+.SH DESCRIPTION
+Unicycler\-scrub \- read trimming, chimera detection and misassembly detection
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR INPUT, \fB\-\-input\fR INPUT
+These are the reads or assembly to be scrubbed (can
+be FASTA or FASTQ format
+.TP
+\fB\-o\fR OUT, \fB\-\-out\fR OUT
+The scrubbed reads or assembly will be saved to this
+file (will have the same format as the \fB\-\-input\fR file
+format) or use "none" to not produce an output file
+.TP
+\fB\-r\fR READS, \fB\-\-reads\fR READS
+These are the reads used to scrub \fB\-\-input\fR (can be
+FASTA or FASTQ format) (default: same file as
+\fB\-\-input\fR)
+.TP
+\fB\-\-trim\fR TRIM
+The aggressiveness with which the input will be
+trimmed (0 to 100, where 0 is no trimming and 100 is
+very aggressive trimming) (default: 50)
+.TP
+\fB\-\-split\fR SPLIT
+The aggressiveness with which the input will be
+split (0 to 100, where 0 is no splitting and 100 is
+very aggressive splitting) (default: 50)
+.TP
+\fB\-\-min_split_size\fR MIN_SPLIT_SIZE
+Parts of split sequences will only be outputted if
+they are at least this big (default: 1000)
+.TP
+\fB\-\-discard_chimeras\fR
+If used, chimeric sequences will be discarded
+instead of split (default: False)
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of threads used (default: 4)
+.TP
+\fB\-\-keep_paf\fR
+Save the alignments to file (makes repeated runs
+faster because alignments can be loaded from file)
+(default: False)
+.TP
+\fB\-\-parameters\fR PARAMETERS
+Low\-level parameters (for debugging use only)
+(default: )
+.TP
+\fB\-\-verbosity\fR VERBOSITY
+Level of stdout information (default: 1)
+.IP
+0 = no stdout,
+.IP
+1 = basic progress indicators,
+.IP
+2 = extra info,
+.IP
+3 = debugging info
+.SH SEE ALSO
+unicycler(1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.