gelog/snap repository overview

⁠Supported tags and respective Dockerfile links

• 1.0beta.15/Dockerfile⁠

⁠What is Snap ?

SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

SNAP was developed by a team from the UC Berkeley AMP Lab, Microsoft, and UCSF.

http://snap.cs.berkeley.edu/⁠

⁠What is Docker?

Docker is an open platform for developers and sysadmins to build, ship, and run distributed applications. Consisting of Docker Engine, a portable, lightweight runtime and packaging tool, and Docker Hub, a cloud service for sharing applications and automating workflows, Docker enables apps to be quickly assembled from components and eliminates the friction between development, QA, and production environments. As a result, IT can ship faster and run the same app, unchanged, on laptops, data center VMs, and any cloud.

https://www.docker.com/whatisdocker/⁠

⁠What is a Docker Image?

Docker images are the basis of containers. Images are read-only, while containers are writeable. Only the containers can be executed by the operating system.

https://docs.docker.com/terms/image/⁠

⁠Dependencies

• Install Docker⁠

⁠Base Docker image

• Ubuntu 14.04 LTS⁠

⁠How to use this image?

⁠1) Get the reference genome (or chromosome) and unzip it.

mkdir /data/
wget -O /data/chr1.fa.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz
gzip -d /data/chr1.fa.gz

⁠2) Index the reference genome (or chromosome)

docker run --rm=true -ti -v /data:/data gelog/snap index /data/chr1.fa /data/snap-index.chr1  

⁠3) Get a genome (or chromosome)

wget -O /data/SRR062634.filt.fastq.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/sequence_read/SRR062634.filt.fastq.gz
gzip -d /data/SRR062634.filt.fastq.gz

⁠4) Align the genome (or chromosome) with Snap

docker run --rm=true -ti -v /data:/data gelog/snap single /data/snap-index.chr1/ /data/SRR062634.filt.fastq -o /data/SRR062634.sam