Introduction

The two key programs that come with Novoalign package are:

Requirements

A computer with an Intel/AMD X86-64 CPU running a 64-bit Linux with 2.6 Kernel or MAC OS-X.

RAM requirements depend on the size of the genome you are aligning against. General rule is about 3 times the size of the reference genome. A minimum of 8Gbyte RAM is recommended for alignments against Human genome.

Getting Started

1. Download Novoalign tar file from www.novocraft.com, just click the I agree button and then look for the latest release named like "Novo Package V2.xx.xx for X86-64 Linux (Static LInk)"
2. Untar with command:

   tar -xzf novo*tar.gz

   This will create a folder ./novocraft with Novoalign programs and some documentation files and perl scripts.
3. Download the Sample Data tar file that is attached to this page.
4. Untar with command:

   tar -xzf sampledata.tar.gz

   This will create a folder ./sampledata with some files that we'll use to run Novoalign

Running Novoalign

Build the indexed genome

./novocraft/novoindex ssuis.nix ./sampledata/S_suis.dna

Run Novoalign for Single End Reads

./novocraft/novoalign -d ssuis.nix -f ./sampledata/s_1_sequence.txt

Run Novoalign for Paired End Reads

./novocraft/novoalign -d ssuis.nix -f ./sampledata/s_1_0000.1.fastq ./sampledata/s_1_0000.2.fastq

Using Novoalign on Bisulphite treated DNA

Build the indexed genome

./novocraft/novoindex -b ssuis.nbx ./sampledata/S_suis.dna

Run Novoalign for Single End Bi-Seq Reads

./novocraft/novoalign -d ssuis.nbx -f ./sampledata/sim_biseq.1.fastq

Run Novoalign for Paired End Bi-Seq Reads

./novocraft/novoalign -d ssuis.nbx -f ./sampledata/sim_biseq.1.fastq ./sampledata/sim_biseq.2.fastq

Using Novoalign on SOLiD(TM) Colorspace reads

Build the indexed genome for SOLiD colorspace alignment

./novocraft/novoindex -c  ssuis.ncx ./sampledata/S_suis.dna

Run Novoalign for Single End SOLiD Reads

./novocraft/novoalignCS -d ssuis.ncx -f reads.csfastq

Run Novoalign for mate-pair SOLiD Reads

./novocraft/novoalignCS -d ssuis.ncx -f file_F3.csfastq file_R3.csfastq

Specify the library insert size and standard deviation of working with mate-pair libraries

./novocraft/novoalignCS -d ssuis.ncx -f file_F3.csfastq file_R3.csfastq -i 3000 200

Note that novoalignCS accepts reads in .csfasta and .csfastq formats.