Contents

[Overview] (#overview)
[Copy right] (#copyright)
[How to cite LEAF?] (#cite)
[Short Manual] (#manual)

### 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. ###Copy right LEAF is under the [Artistic License 2.0](http://opensource.org/licenses/Artistic-2.0). ### How to cite LEAF? If you use LEAF, please cite the following paper: Not available yet... ### 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

   Aligners Bowtie2 and BLAT are required to run LEAF.
   The downloaded LEAF.cpp file can be compiled with command g++ -o LEAF LEAF.cpp -lpthread.

3. Inputs

   • Paired-end DNA reads in FASTA format.
   • De novo contigs assembled by any de novo DNA-Seq assembler (Velvet, ABySS, etc.).
   • 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

   • Extended contigs in FASTA format.
   • Remaining contigs not extended in FASTA format.