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?

Requirements

• GCC ≥ 4.4.7
• zlib

Using conda

lordFast can be installed using conda package manager via bioconda channel:

$ 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 lordfast.

$ cd lordfast
$ make

How to run?

SYNOPSIS

lordfast --index FILE [OPTIONS]
lordfast --search FILE --seq FILE [OPTIONS]

OPTIONS

Run lordfast -h or man ./HELP.man to see available options.

Indexing options

-I, --index STR
    Path to the reference genome file in FASTA format which is supposed to be indexed. [required]

Mapping options

-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]

Advanced options

-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.

Other options

-h, --help
    Prints this help file.

-v, --version
    Prints the version of software.

EXAMPLES

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

Publication

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

Bugs

Please report the bugs through lordFAST's issues page at https://github.com/vpc-ccg/lordfast/issues.

Contact

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