LEAF: leveraging reference genome to boost DNA-Seq assemblies
Author: Ergude Bao
Overview
LEAF is a software that leverages reference genome from a closely related species to extend/join contigs pre-assembled with any de novo DNA-Seq assembler.
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Downloads and Version History
Short Manual
1. System requirements
LEAF is suitable for 32-bit or 64-bit machines with Linux operating systems. At least 4GB of system memory is recommended for assembling larger data sets.
2. Installation
The downloaded LEAF.cpp file can be compiled with command g++ -o LEAF LEAF.cpp -lpthread.
3. Inputs
(1) Paired-end DNA reads in FASTA format.
(2) De novo contigs assembled by any de novo DNA-Seq assembler (Velvet, ABySS, etc.).
(3) Reference genome from a closely related species.
4. Using LEAF
LEAF --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow distanceLow --distanceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa [--kMer k --insertVariation insertVariation --coverage coverage --noAlignment --part p]
Inputs:
--read1 is the the first pair of PE DNA reads in fasta format
--read2 is the the second pair of PE DNA reads in fasta format
--contig is the initial contigs in fasta format
--genome is the reference genome in fasta format
--distanceLow is the lower bound of alignment distance between the first and second pairs of PE DNA reads
--distanceHigh is the upper bound of alignment distance between the first and second pairs of PE DNA reads
Outputs:
--extendedContig is the extended contig file in fasta format
--remainingContig is the not extended initial contig file in fasta format
Options:
--kMer is the k-mer size (default: 5)
--insertVariation is the standard variation of insert length (default: 100)
--coverage is the minimum coverage to keep a path in de Bruijn graph (default: 20)
--noAlignment skips the initial time-consuming alignment step, if all the alignment files have been provided in tmp directory (default: none)
--part is the number of parts a chromosome is divided into when it is loaded to reduce memory requirement (default: 1)
5. Outputs
(1) Extended contigs in FASTA format.
(2) Remaining contigs not extended in FASTA format.
