BItsliced Genomic Signature Index [bigsi]

BItsliced Genomic Signature Index [BIGSI] Docs

Welcome to the BIGSI documentation. You'll find comprehensive guides and documentation to help you start working with BIGSI as quickly as possible.

BIGSIs–BItsliced Genomic Signature Indexes–allow for efficient indexing and search in very large collections of WGS data, in particular bacterial or viral data sets WGS data sets. BIGSI can index and query raw, or assembled data.

A prebuilt index is available for download at http://ftp.ebi.ac.uk/pub/software/bigsi/nat_biotech_2018/all-microbial-index-v03/ or a hosted demo is available here http://www.bigsi.io/.

Please cite our paper if you use this tool in your research:
'Ultra-fast search of all deposited bacterial and viral genomic data' http://dx.doi.org/10.1038/s41587-018-0010-1

Get Started    Guides

Requirements

BIGSI requires that you have Berkeley-DB version 4.8.30 installed. We also recommend installing mccortex to assist with the preprocessing of the data.

To install Berkeley-DB backend:

export BERKELEYDB_DIR=~/usr/local/
export BERKELEY_VERSION=4.8.30
# Download, configure and install BerkeleyDB
wget -P /tmp http://download.oracle.com/berkeley-db/db-"${BERKELEY_VERSION}".tar.gz 
tar -xf /tmp/db-"${BERKELEY_VERSION}".tar.gz -C /tmp
rm -f /tmp/db-"${BERKELEY_VERSION}".tar.gz
cd /tmp/db-"${BERKELEY_VERSION}"/build_unix 
../dist/configure --prefix $BERKELEYDB_DIR && make && make install
pip3 install cython
pip3 install bsddb3

To install rockdb backend follow instructions:
https://github.com/twmht/python-rocksdb

git clone https://github.com/Phelimb/BIGSI.git
cd BIGSI
pip3 install -r requirements.txt
pip3 install -r optional-requirements.txt
pip3 install .

Linux


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