[med-svn] [spades] 01/03: add man page sources
Sascha Steinbiss
sascha at steinbiss.name
Thu Feb 11 16:01:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository spades.
commit 2192d1991343edf872c4abb72c819578012bf31c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu Feb 11 15:58:46 2016 +0000
add man page sources
---
debian/man_src/dipspades.1.ronn | 131 ++++++++++++++++++++++++++++++++++++++++
debian/man_src/spades.1.ronn | 128 +++++++++++++++++++++++++++++++++++++++
debian/man_src/truspades.1.ronn | 42 +++++++++++++
3 files changed, 301 insertions(+)
diff --git a/debian/man_src/dipspades.1.ronn b/debian/man_src/dipspades.1.ronn
new file mode 100644
index 0000000..c2fc846
--- /dev/null
+++ b/debian/man_src/dipspades.1.ronn
@@ -0,0 +1,131 @@
+dipspades(1) -- diploid genome assembler
+========================================
+
+## SYNOPSIS
+
+`dipspades` [options] -o <output_dir>
+
+## DESCRIPTION
+
+`dipspades` is the main executable for the **dipSPAdes** software, a genome
+assembler designed for diploid genomes with a high heterozygosity rate. It
+assembles genomic reads given to it and places the resulting assembly in
+<output_dir>.
+
+## OPTIONS
+
+### Basic options
+
+ * `-o` <output_dir>:
+ directory to store all the resulting files (required)
+
+ * `--iontorrent`:
+ this flag is required for IonTorrent data
+
+ * `--test`:
+ runs dipSPAdes on toy dataset
+
+ * `-h`/`--help`:
+ prints this usage message
+
+### Input data
+
+ * `--12` <filename>:
+ file with interlaced forward and reverse paired-end reads
+
+ * `-1` <filename>:
+ file with forward paired-end reads
+
+ * `-2` <filename>:
+ file with reverse paired-end reads
+
+ * `-s` <filename>:
+ file with unpaired reads
+
+ * `--pe<#>-12` <filename>:
+ file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+
+ * `--pe<#>-1` <filename>:
+ file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-2` <filename>:
+ file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-s` <filename>:
+ file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-<or>`:
+ orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--s<#>` <filename>:
+ file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-12` <filename>:
+ file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-1` <filename>:
+ file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-2` <filename>:
+ file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-s` <filename>:
+ file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-<or>`:
+ orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--hqmp<#>-12` <filename>:
+ file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-1` <filename>:
+ file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-2` <filename>:
+ file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-s` <filename>:
+ file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-<or>`:
+ orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--nxmate<#>-1` <filename>:
+ file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
+ * `--nxmate<#>-2` <filename>:
+ file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
+ * `--sanger` <filename>:
+ file with Sanger reads
+ * `--pacbio` <filename>:
+ file with PacBio reads
+ * `--nanopore` <filename>:
+ file with Nanopore reads
+ * `--trusted-contigs` <filename>:
+ file with trusted contigs
+ * `--untrusted-contigs` <filename>:
+ file with untrusted contigs
+
+### Input haplocontigs
+
+ * `--hap` <filename>:
+ file with haplocontigs
+
+### Pipeline options
+
+ * `--only-assembler`:
+ runs only assembling (without read error correction)
+ * `--disable-gzip-output`:
+ forces error correction not to compress the corrected reads
+ * `--disable-rr`:
+ disables repeat resolution stage of assembling
+
+### dipSPAdes options
+
+ * `--expect-gaps`:
+ indicates that significant number of gaps in coverage is expected
+ * `--expect-rearrangements`:
+ indicates that significant number of rearrangements between haplomes of diploid genome is expected
+ * `--hap-assembly`:
+ enables haplotype assembly phase
+
+### Advanced options
+
+ * `--dataset` <filename>:
+ file with dataset description in YAML format
+ * `-t`/`--threads` <int>:
+ number of threads [default: 16]
+ * `-m`/`--memory` <int>:
+ RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
+ * `--tmp-dir` <dirname>:
+ directory for temporary files [default: <output_dir>/tmp]
+ * `-k` <int,int,...>:
+ comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']
+ * `--cov-cutoff` <float>:
+ coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
+ * `--phred-offset` <33 or 64>:
+ PHRED quality offset in the input reads (33 or 64) [default: auto-detect]
diff --git a/debian/man_src/spades.1.ronn b/debian/man_src/spades.1.ronn
new file mode 100644
index 0000000..71adcf9
--- /dev/null
+++ b/debian/man_src/spades.1.ronn
@@ -0,0 +1,128 @@
+spades(1) -- SPAdes genome assembler
+====================================
+
+## SYNOPSIS
+
+`spades` [options] -o <output_dir>
+
+## DESCRIPTION
+
+`spades` is the main executable for the **SPAdes** software. It
+assembles genomic reads given to it and places the resulting assembly in
+<output_dir>.
+
+## OPTIONS
+
+### Basic options
+
+ * `-o` <output_dir>:
+ directory to store all the resulting files (required)
+
+ * `--sc`:
+ this flag is required for MDA (single-cell) data
+
+ * `--iontorrent`:
+ this flag is required for IonTorrent data
+
+ * `--test`:
+ runs SPAdes on toy dataset
+
+ * `-h`/`--help`:
+ prints this usage message
+
+### Input data
+
+ * `--12` <filename>:
+ file with interlaced forward and reverse paired-end reads
+
+ * `-1` <filename>:
+ file with forward paired-end reads
+
+ * `-2` <filename>:
+ file with reverse paired-end reads
+
+ * `-s` <filename>:
+ file with unpaired reads
+
+ * `--pe<#>-12` <filename>:
+ file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+
+ * `--pe<#>-1` <filename>:
+ file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-2` <filename>:
+ file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-s` <filename>:
+ file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
+ * `--pe<#>-<or>`:
+ orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--s<#>` <filename>:
+ file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-12` <filename>:
+ file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-1` <filename>:
+ file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-2` <filename>:
+ file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-s` <filename>:
+ file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--mp<#>-<or>`:
+ orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--hqmp<#>-12` <filename>:
+ file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-1` <filename>:
+ file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-2` <filename>:
+ file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-s` <filename>:
+ file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
+ * `--hqmp<#>-<or>`:
+ orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
+ * `--nxmate<#>-1` <filename>:
+ file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
+ * `--nxmate<#>-2` <filename>:
+ file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
+ * `--sanger` <filename>:
+ file with Sanger reads
+ * `--pacbio` <filename>:
+ file with PacBio reads
+ * `--nanopore` <filename>:
+ file with Nanopore reads
+ * `--trusted-contigs` <filename>:
+ file with trusted contigs
+ * `--untrusted-contigs` <filename>:
+ file with untrusted contigs
+
+### Pipeline options
+
+ * `--only-error-correction`:
+ runs only read error correction (without assembling)
+ * `--only-assembler`:
+ runs only assembling (without read error correction)
+ * `--careful`:
+ tries to reduce number of mismatches and short indels
+ * `--continue`:
+ continue run from the last available check-point
+ * `--restart-from` <cp>:
+ restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
+ * `--disable-gzip-output`:
+ forces error correction not to compress the corrected reads
+ * `--disable-rr`:
+ disables repeat resolution stage of assembling
+
+### Advanced options
+
+ * `--dataset` <filename>:
+ file with dataset description in YAML format
+ * `-t`/`--threads` <int>:
+ number of threads [default: 16]
+ * `-m`/`--memory` <int>:
+ RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
+ * `--tmp-dir` <dirname>:
+ directory for temporary files [default: <output_dir>/tmp]
+ * `-k` <int,int,...>:
+ comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']
+ * `--cov-cutoff` <float>:
+ coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
+ * `--phred-offset` <33 or 64>:
+ PHRED quality offset in the input reads (33 or 64) [default: auto-detect]
+
diff --git a/debian/man_src/truspades.1.ronn b/debian/man_src/truspades.1.ronn
new file mode 100644
index 0000000..ac4b443
--- /dev/null
+++ b/debian/man_src/truspades.1.ronn
@@ -0,0 +1,42 @@
+truspades(1) -- truSPAdes genome assembler
+==========================================
+
+## SYNOPSIS
+
+`truspades` [options] -o <output_dir>
+
+## DESCRIPTION
+
+`truspades` is the main executable for the **truSPAdes** software. It
+assembles genomic reads given to it and places the resulting assembly in
+<output_dir>.
+
+## OPTIONS
+
+### Basic options
+
+ * `-o` <output_dir>:
+ directory to store all the resulting files (required)
+
+ * `--test`:
+ runs truSPAdes on toy dataset
+
+ * `-h`/`--help`:
+ prints this usage message
+
+ * `-t`/`--threads` <int>:
+ number of threads
+
+ * `--continue`:
+ continue interrupted launch
+
+ * `--construct-dataset`:
+ parse dataset from input folder
+
+### Input options
+
+ * `--input-dir` <directory>:
+ directory with input data. Note that the directory should contain only files with reads. This option can be used several times to provide several input directories.
+
+ * `--dataset` <file>:
+ file with dataset description
--
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