[med-svn] [Git][med-team/megahit][master] Manpages. Will refine the outputs soon
Shayan Doust
gitlab at salsa.debian.org
Fri Oct 11 00:50:37 BST 2019
Shayan Doust pushed to branch master at Debian Med / megahit
Commits:
d72c2a08 by Shayan Doust at 2019-10-10T23:49:22Z
Manpages. Will refine the outputs soon
- - - - -
6 changed files:
- + debian/manpages
- + debian/mans/megahit.1
- + debian/mans/megahit_core.1
- + debian/mans/megahit_core_no_hw_accel.1
- + debian/mans/megahit_core_popcnt.1
- + debian/mans/megahit_toolkit.1
Changes:
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/mans/*.1
=====================================
debian/mans/megahit.1
=====================================
@@ -0,0 +1,141 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH MEGAHIT "1" "October 2019" "megahit 1.2.8" "User Commands"
+.SH NAME
+megahit \- ultra-fast and memory-efficient meta-genome assembler
+.SH DESCRIPTION
+MEGAHIT v1.2.8
+.PP
+contact: Dinghua Li <voutcn at gmail.com>
+.SS "Usage:"
+.IP
+megahit [options] {\-1 <pe1> \fB\-2\fR <pe2> | \fB\-\-12\fR <pe12> | \fB\-r\fR <se>} [\-o <out_dir>]
+.IP
+Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)
+.TP
+\fB\-1\fR
+<pe1> comma\-separated list of fasta/q paired\-end #1 files, paired with files in <pe2>
+.TP
+\fB\-2\fR
+<pe2> comma\-separated list of fasta/q paired\-end #2 files, paired with files in <pe1>
+.TP
+\fB\-\-12\fR
+<pe12> comma\-separated list of interleaved fasta/q paired\-end files
+.TP
+\fB\-r\fR/\-\-read
+<se> comma\-separated list of fasta/q single\-end files
+.SS "Optional Arguments:"
+.IP
+Basic assembly options:
+.TP
+\fB\-\-min\-count\fR
+<int> minimum multiplicity for filtering (k_min+1)\-mers [2]
+.TP
+\fB\-\-k\-list\fR
+<int,int,..> comma\-separated list of kmer size
+all must be odd, in the range 15\-255, increment <= 28)
+[21,29,39,59,79,99,119,141]
+.IP
+Another way to set \fB\-\-k\-list\fR (overrides \fB\-\-k\-list\fR if one of them set):
+.TP
+\fB\-\-k\-min\fR
+<int> minimum kmer size (<= 255), must be odd number [21]
+.TP
+\fB\-\-k\-max\fR
+<int> maximum kmer size (<= 255), must be odd number [141]
+.TP
+\fB\-\-k\-step\fR
+<int> increment of kmer size of each iteration (<= 28), must be even number [12]
+.IP
+Advanced assembly options:
+.TP
+\fB\-\-no\-mercy\fR
+do not add mercy kmers
+.TP
+\fB\-\-bubble\-level\fR
+<int> intensity of bubble merging (0\-2), 0 to disable [2]
+.TP
+\fB\-\-merge\-level\fR
+<l,s> merge complex bubbles of length <= l*kmer_size and similarity >= s [20,0.95]
+.TP
+\fB\-\-prune\-level\fR
+<int> strength of low depth pruning (0\-3) [2]
+.TP
+\fB\-\-prune\-depth\fR
+<int> remove unitigs with avg kmer depth less than this value [2]
+.TP
+\fB\-\-disconnect\-ratio\fR
+<float> disconnect unitigs if its depth is less than this ratio times
+the total depth of itself and its siblings [0.1]
+.TP
+\fB\-\-low\-local\-ratio\fR
+<float> remove unitigs if its depth is less than this ratio times
+the average depth of the neighborhoods [0.2]
+.TP
+\fB\-\-max\-tip\-len\fR
+<int> remove tips less than this value [2*k]
+.TP
+\fB\-\-cleaning\-rounds\fR
+<int> number of rounds for graph cleanning [5]
+.TP
+\fB\-\-no\-local\fR
+disable local assembly
+.TP
+\fB\-\-kmin\-1pass\fR
+use 1pass mode to build SdBG of k_min
+.IP
+Presets parameters:
+.TP
+\fB\-\-presets\fR
+<str> override a group of parameters; possible values:
+meta\-sensitive: '\-\-min\-count 1 \fB\-\-k\-list\fR 21,29,39,49,...,129,141'
+meta\-large: '\-\-k\-min 27 \fB\-\-k\-max\fR 127 \fB\-\-k\-step\fR 10'
+(large & complex metagenomes, like soil)
+.IP
+Hardware options:
+.TP
+\fB\-m\fR/\-\-memory
+<float> max memory in byte to be used in SdBG construction
+(if set between 0\-1, fraction of the machine's total memory) [0.9]
+.TP
+\fB\-\-mem\-flag\fR
+<int> SdBG builder memory mode. 0: minimum; 1: moderate;
+others: use all memory specified by '\-m/\-\-memory' [1]
+.TP
+\fB\-t\fR/\-\-num\-cpu\-threads
+<int> number of CPU threads [# of logical processors]
+.TP
+\fB\-\-no\-hw\-accel\fR
+run MEGAHIT without BMI2 and POPCNT hardware instructions
+.IP
+Output options:
+.TP
+\fB\-o\fR/\-\-out\-dir
+<string> output directory [./megahit_out]
+.TP
+\fB\-\-out\-prefix\fR
+<string> output prefix (the contig file will be OUT_DIR/OUT_PREFIX.contigs.fa)
+.TP
+\fB\-\-min\-contig\-len\fR
+<int> minimum length of contigs to output [200]
+.TP
+\fB\-\-keep\-tmp\-files\fR
+keep all temporary files
+.TP
+\fB\-\-tmp\-dir\fR
+<string> set temp directory
+.SS "Other Arguments:"
+.TP
+\fB\-\-continue\fR
+continue a MEGAHIT run from its last available check point.
+please set the output directory correctly when using this option.
+.TP
+\fB\-\-test\fR
+run MEGAHIT on a toy test dataset
+.TP
+\fB\-h\fR/\-\-help
+print the usage message
+.TP
+\fB\-v\fR/\-\-version
+print version
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/megahit_core.1
=====================================
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH MEGAHIT_CORE "1" "October 2019" "megahit_core 1.2.8" "User Commands"
+.SH NAME
+megahit_core \- ultra-fast and memory-efficient meta-genome assembler
+.SH SYNOPSIS
+.B megahit_core
+\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]
+.SH DESCRIPTION
+.IP
+sub\-programs:
+.TP
+assemble
+assemble from SdBG
+.TP
+local
+local asssembly
+.TP
+iterate
+extract iterative edges
+.TP
+buildlib
+build read library
+.TP
+count
+kmer counting
+.TP
+read2sdbg
+build sdbg from reads
+.TP
+seq2sdbg
+build sdbg from megahit contigs + edges
+.TP
+contig2fastg
+convert MEGAHIT's k*.contigs.fa to fastg format
+.TP
+readstat
+calculate read stats (# of reads, bases, longest, shortest, average)
+.TP
+filterbylen
+filter contigs by length
+.TP
+checkcpu
+check whether the run\-time CPU supports POPCNT and BMI2
+.TP
+checkpopcnt
+check whether the run\-time CPU supports POPCNT
+.TP
+checkbmi2
+check whether the run\-time CPU supports BMI2
+.TP
+dumpversion
+dump version
+.TP
+kmax
+the largest k value supported
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/megahit_core_no_hw_accel.1
=====================================
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH MEGAHIT_CORE_NO_HW_ACCEL "1" "October 2019" "megahit_core_no_hw_accel 1.2.8" "User Commands"
+.SH NAME
+megahit_core_no_hw_accel \- ultra-fast and memory-efficient meta-genome assembler
+.SH SYNOPSIS
+.B megahit_core_no_hw_accel
+\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]
+.SH DESCRIPTION
+.IP
+sub\-programs:
+.TP
+assemble
+assemble from SdBG
+.TP
+local
+local asssembly
+.TP
+iterate
+extract iterative edges
+.TP
+buildlib
+build read library
+.TP
+count
+kmer counting
+.TP
+read2sdbg
+build sdbg from reads
+.TP
+seq2sdbg
+build sdbg from megahit contigs + edges
+.TP
+contig2fastg
+convert MEGAHIT's k*.contigs.fa to fastg format
+.TP
+readstat
+calculate read stats (# of reads, bases, longest, shortest, average)
+.TP
+filterbylen
+filter contigs by length
+.TP
+checkcpu
+check whether the run\-time CPU supports POPCNT and BMI2
+.TP
+checkpopcnt
+check whether the run\-time CPU supports POPCNT
+.TP
+checkbmi2
+check whether the run\-time CPU supports BMI2
+.TP
+dumpversion
+dump version
+.TP
+kmax
+the largest k value supported
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/megahit_core_popcnt.1
=====================================
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH MEGAHIT_CORE_POPCNT "1" "October 2019" "megahit_core_popcnt 1.2.8" "User Commands"
+.SH NAME
+megahit_core_popcnt \- ultra-fast and memory-efficient meta-genome assembler
+.SH SYNOPSIS
+.B megahit_core_popcnt
+\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]
+.SH DESCRIPTION
+.IP
+sub\-programs:
+.TP
+assemble
+assemble from SdBG
+.TP
+local
+local asssembly
+.TP
+iterate
+extract iterative edges
+.TP
+buildlib
+build read library
+.TP
+count
+kmer counting
+.TP
+read2sdbg
+build sdbg from reads
+.TP
+seq2sdbg
+build sdbg from megahit contigs + edges
+.TP
+contig2fastg
+convert MEGAHIT's k*.contigs.fa to fastg format
+.TP
+readstat
+calculate read stats (# of reads, bases, longest, shortest, average)
+.TP
+filterbylen
+filter contigs by length
+.TP
+checkcpu
+check whether the run\-time CPU supports POPCNT and BMI2
+.TP
+checkpopcnt
+check whether the run\-time CPU supports POPCNT
+.TP
+checkbmi2
+check whether the run\-time CPU supports BMI2
+.TP
+dumpversion
+dump version
+.TP
+kmax
+the largest k value supported
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/mans/megahit_toolkit.1
=====================================
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH MEGAHIT_TOOLKIT "1" "October 2019" "megahit_toolkit 1.2.8" "User Commands"
+.SH NAME
+megahit_toolkit \- ultra-fast and memory-efficient meta-genome assembler
+.SH SYNOPSIS
+.B megahit_toolkit
+\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]
+.SH DESCRIPTION
+.IP
+sub\-programs:
+.TP
+assemble
+assemble from SdBG
+.TP
+local
+local asssembly
+.TP
+iterate
+extract iterative edges
+.TP
+buildlib
+build read library
+.TP
+count
+kmer counting
+.TP
+read2sdbg
+build sdbg from reads
+.TP
+seq2sdbg
+build sdbg from megahit contigs + edges
+.TP
+contig2fastg
+convert MEGAHIT's k*.contigs.fa to fastg format
+.TP
+readstat
+calculate read stats (# of reads, bases, longest, shortest, average)
+.TP
+filterbylen
+filter contigs by length
+.TP
+checkcpu
+check whether the run\-time CPU supports POPCNT and BMI2
+.TP
+checkpopcnt
+check whether the run\-time CPU supports POPCNT
+.TP
+checkbmi2
+check whether the run\-time CPU supports BMI2
+.TP
+dumpversion
+dump version
+.TP
+kmax
+the largest k value supported
+.SH AUTHOR
+This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0
--
View it on GitLab: https://salsa.debian.org/med-team/megahit/commit/d72c2a0808ddcc96a2fe8a26e80d6b03c2133bb0
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