libra

Compute the Similarity between Metagenomic Samples

DOWNLOAD BINARY

Download a pre-built binary (compiled with Java 7, including dependencies):

• Libra v1.2.8 stable

For old releases, check out the release page:

• Libra Releases

BUILD FROM SOURCE

Most users do not need to build a binary from source. Use pre-built binaries.

To build, use ANT build system.

Type following to build without dependencies:

ant

Type following to build with dependencies (recommended):

ant allinone

The jar package built will be located at the /dist directory.

RUN

Preprocessing FASTA/FASTQ files

hadoop jar libra-all.jar preprocess -k 20 -t 8 -o /index_dir /source_dir

Preprocessing Options

• k : k-mer size
• t : number of tasks (reducers). 1 by default.
• s : min size of group in bytes. 10GB by default. For each file group, a separate index file is created.
• g : max number of groups. 20 groups by default. If groups to be created by "-s" option exceeds this value, combine groups.
• f : kmer filter algorithm. NONE | STDDEV (standard deviation) | STDDEV2 (two's standard deviation) | NOTUNIQUE (default)
• o : output directory

Scoring

hadoop jar libra-all.jar core -w LOGARITHM -o /score_dir /index_dir

Scoring Options

• s : scoring algorithm. COSINESIMILARITY (default) | BRAYCURTIS | JENSENSHANNON
• m : run mode. MAP (default) | REDUCE
• w : weighting algorithm. LOGARITHM (default) | BOOLEAN | NATURAL
• o : output directory