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HELP.man
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.TH lordFAST 1 "Last Updated: June 26, 2018" lordFAST "lordfast Manual"
.SH NAME
lordfast
.SH DESCRIPTION
lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.
.SH INSTALLATION
lordFast can be installed using conda package manager (via bioconda channel) using the following command:
.br
$ conda install -c bioconda lordfast
In order to build from source, please download the latest release from
.br
https://github.com/vpc-ccg/lordfast/releases
.br
or alternatively clone the repository by running the following command:
.br
$ git clone https://github.com/vpc-ccg/lordfast.git
Now the code can be compiled easily by running "make" command line which builds the binary file "lordfast".
.br
$ cd lordfast
.br
$ make
.SH SYNOPSIS
lordfast --index FILE [OPTIONS]
.br
lordfast --search FILE --seq FILE [OPTIONS]
.SH OPTIONS
.br
.SS Indexing options
.TP
.BI "-I, --index " STR
Path to the reference genome file in FASTA format which is supposed to be indexed. [required]
.br
.SS Mapping options
.TP
.BI "-S, --search " STR
Path to the reference genome file in FASTA format. [required]
.TP
.BI "-s, --seq " STR
Path to the file containing read sequences in FASTA/FASTQ format. [required]
.TP
.BI "-o, --out " STR
Write output to
.I STR
file rather than standard output. [stdout]
.TP
.BI "-t, --threads " INT
Use
.I INT
number of CPU cores. Pass 0 to use all the available cores. [1]
.br
.SS Advanced options
.TP
.BI "-k, --minAnchorLen " INT
Minimum required length of anchors to be considered. [14]
.TP
.BI "-n, --numMap " INT
Perform alignment for at most
.I INT
candidates. [10]
.TP
.BI "-l, --minReadLen " INT
Do not try to map any read shorter than
.I INT
bp and report them as unmapped. [1000]
.TP
.BI "-c, --anchorCount " INT
Consider
.I INT
anchoring positions on the long read. [1000]
.TP
.BI "-m, --maxRefHit " INT
Ignore anchoring positions with more than
.I INT
reference hits. [1000]
.TP
.BI "-R, --readGroup " STR
SAM read group line in a format like '@RG\tID:foo\tSM:bar'. []
.TP
.BI "-a, --chainAlg " INT
Chaining algorithm to use. Options are "dp-n2" and "clasp". [dp-n2]
.TP
.BI "--noSamHeader "
Do not print sam header in the output.
.br
.SS Other options
.TP
.B -h, --help
Print this help file.
.TP
.B -v, --version
Print the version of software.
.SH EXAMPLES
Indexing the reference genome:
.br
$ ./lordfast --index gen.fa
Mapping to the reference genome:
.br
$ ./lordfast --search gen.fa --seq reads.fastq > map.sam
.br
$ ./lordfast --search gen.fa --seq reads.fastq --threads 4 > map.sam
.SH BUGS
Please report the bugs through lordfast's issues page at
.br
https://github.com/vpc-ccg/lordfast/issues
.SH CONTACT
Ehsan Haghshenas ([email protected])
.SH COPYRIGHT AND LICENSE
This software is released under GNU General Public License (v3.0)
.br
Copyright (c) 2018 Simon Fraser University, All rights reserved.