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.
- GCC ≥ 4.4.7
- zlib
lordFast can be installed using conda package manager via bioconda channel:
$ conda install -c bioconda lordfast
In order to build lordFAST, please download the latest release from https://github.com/vpc-ccg/lordfast/releases or alternatively clone the repository by running the following command:
$ 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.
$ cd lordfast
$ make
lordfast --index FILE [OPTIONS]
lordfast --search FILE --seq FILE [OPTIONS]
Run lordfast -h or man ./HELP.man to see available options.
-I, --index STR
Path to the reference genome file in FASTA format which is supposed to be indexed. [required]
-S, --search STR
Path to the reference genome file in FASTA format. [required]
-s, --seq STR
Path to the file containing read sequences in FASTA/FASTQ format. [required]
-o, --out STR
Write output to STR file rather than standard output. [stdout]
-t, --threads INT
Use INT number of CPU cores. Pass 0 to use all the available cores. [1]
-k, --minAnchorLen INT
Minimum required length of anchors to be considered. [14]
-n, --numMap INT
Perform alignment for at most INT candidates. [10]
-l, --minReadLen INT
Do not try to map any read shorter than INT bp and report them as unmapped. [1000]
-c, --anchorCount INT
Consider INT anchoring positions on the long read. [1000]
-m, --maxRefHit INT
Ignore anchoring positions with more than INT reference hits. [1000]
-R, --readGroup STR
SAM read group line in a format like '@RG\tID:foo\tSM:bar'. []
-a, --chainAlg INT
Chaining algorithm to use. Options are "dp-n2" and "clasp". [dp-n2]
--noSamHeader
Do not print sam header in the output.
-h, --help
Prints this help file.
-v, --version
Prints the version of software.
$ ./lordfast --index refgen.fasta
$ ./lordfast --search refgen.fa --seq reads.fastq > map.sam
$ ./lordfast --search refgen.fa --seq reads.fastq --threads 4 > map.sam
Haghshenas E., Sahinalp S.C. and Hach F., "lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data" Bioinformatics (2018) DOI: 10.1093/bioinformatics/bty544
Please report the bugs through lordFAST's issues page at https://github.com/vpc-ccg/lordfast/issues.
Ehsan Haghshenas (ehaghshe AT sfu DOT ca)
This software is released under GNU General Public License (v3.0)
Copyright (c) 2018 Simon Fraser University
- BWA (used for the BWT-based index) is developed by Heng Li and is licensed under GPL
- Edlib (used for global alignment) is developed by Martin Sosic and is licensed under MIT
- ksw (used for alignment extension) is licensed under MIT
- clasp (can be used for chaining) is developed and copyrighted by Christian Otto