Ultralightweight NGS Server

Converts BAM and VCF files to json for consumption by a web application

install for mac and linux (no windows)

download and install cmake
run "gem install ngs_server" in the terminal

usage

  # in terminal
  ngs_server --help

  # add data directories to be served
  ngs_server add path-to-dir

  # start server
  ngs_server start
  ngs_server start --port 3000
  # daemonize
  ngs_server start -d

  # stop server if daemonized
  ngs_server stop

access data

see available data sources

invoke file: hg18.bam with coordinates 1 to 100000 on chromosome 22

http://0.0.0.0:4569/json/bam/hg.18?min=1&max=10000&segment=22

vcf files must be compressed with index (see tabix)
invoke file: genotypes.vcf.gz with coordinates 1073361 to 1238825 on chromosome 1

http://0.0.0.0:4569/json/vcf/genotypes.vcf.gz?segment=1&min=1073361&max=1238825

Example

# create data directory
mkdir example-data && cd example-data

# download bam file and index
wget http://bioinformatics.bc.edu/marthlab/download/small.bam
wget http://bioinformatics.bc.edu/marthlab/download/small.bam.bai

# add data directory to ngs_server to be served
cd ../
ngs_server add example-data/

# start server
ngs_server start -p 4569

# paste following url in browser
# to download region of bam as json in web browser
# http://0.0.0.0:4569/json/bam/example-data/small.bam?min=14596532&max=14699000&segment=22