QuickStart

Download and install

Navigate to a directory where you would like MOSAIK to live and then type the following commands: git clone https://github.com/wanpinglee/MOSAIK.git

cd MOSAIK/src

for MAC users: export BLD_PLATFORM=macosx or export BLD_PLATFORM=macosx64

make

The executable MosaikBuild, MosaikAligner, and MosaikJump should be seen in MOSAIK/bin.

Align reads

# Against a large genome (> 100 million basepairs)

MosaikBuild -fr ref.fasta -oa ref.dat

MosaikJump -ia ref.dat -hs 15 -out ref_15

MosaikBuild -q mate1.fastq -q2 mate2.fastq -st illumina -mfl 500 -out read.mkb

(for singled-end) MosaikBuild -q mate1.fastq -st illumina -out read.mkb

MosaikAligner -in read.mkb -out read.mka -ia ref.dat -j ref_15 -annpe pe.ann -annse se.ann

# Against a small genome (< 100 million basepairs)

MosaikBuild -fr ref.fasta -oa ref.dat

MosaikBuild -q mate1.fastq -q2 mate2.fastq -st illumina -mfl 500 -out read.mkb

(for singled-end) MosaikBuild -q mate1.fastq -st illumina -out read.mkb

MosaikAligner -in read.mkb -out read.mka -ia ref.dat -annpe pe.ann -annse se.ann

Note

1. pe.ann and se.ann are on MOSAIK/src/networkFile/.
2. read.mka.bam is the resultant bam while other outputted bams are for other purposes.

Help!

For MOSAIK related questions, please send Wan-Ping Email, wanping.lee@bc.edu.