lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
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.
How to install?
- GCC ≥ 4.4.7
$ conda install -c bioconda lordfast
From source code
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
$ cd lordfast $ make
How to run?
lordfast --index FILE [OPTIONS] lordfast --search FILE --seq FILE [OPTIONS]
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. 
-k, --minAnchorLen INT Minimum required length of anchors to be considered.  -n, --numMap INT Perform alignment for at most INT candidates.  -l, --minReadLen INT Do not try to map any read shorter than INT bp and report them as unmapped.  -c, --anchorCount INT Consider INT anchoring positions on the long read.  -m, --maxRefHit INT Ignore anchoring positions with more than INT reference hits.  -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.
Indexing reference genome:
$ ./lordfast --index refgen.fasta
Mapping to the reference genome:
$ ./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)
Copyright and License
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