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Kourami is a graph-guided assembler for HLA haplotypes covering typing exons (exons 2 and 3 for Class I and exon 3 for Class II) using high-coverage whole genome sequencing data. Kourami constructs highly accurate haplotype sequences at 1-bp resolution by first encoding currently available HLA allelic sequences from IPD-IMGT/HLA Database ( http://www.ebi.ac.uk/ipd/imgt/hla/ ) as partial-ordered graphs. Each database allele is naturally encoded as a path through the graph and any detectable genetic variations (SNPs or indels) not captured by the known sequences are added to the graph by graph-modification based on read alignment to capture differences novel alleles have compared to known sequences. Unlike previously available WGS-based HLA typing methods (database-matching techniques), Kourami direclty assembles both haplotypes for each HLA gene (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1). It also provides the typing result (6-digit 'G' resolution) by outputing the best matching alleles among the known sequences.
The latest release, including both jar and source code can be downloaded from here.
To install Kourami, you must have following installed on your system:
-
JDK 1.8+
-
Apache Maven (3.3+) or Apache Ant (1.9+) is required (we recommend Maven for easy dependency downloads)
- OR you must have dependencies downloaded and added to your CLASSPATH. Then you can compile using javac.
- To use Ant, you must have dependencies downloaded and place jars under 'exjars' directory. 'exjars' directory must be created.
-Download a copy of the preformatted IMGT-HLA database from here and untar it under kourami installation directory.
[MAVEN USERS] To compile and generate a jar file run the following command from the kourami directory where pom.xml is located.
mvn install
[ANT USERS] To compile and generate a jar file run the following command from the kourami directory where build.xml is located.
ant compile jar
This will create a "target" directory and place a packaged jar file in it.
java -jar <PATH_TO>/Kourami.jar [options] <bam-1> ... <bam-n>
NOTE: kourami jar takes a bam aligned to Kourami reference panel built from IMGT/HLA db (included in the preformatted IMGT-HLA database). Detailed notes on how to generate input bam consisting of HLA loci reads aligned to known alleles is explained in How to prepare input bam and HLA panel for Kourami.
| Option Tag | Description |
|---|---|
| -h,--help | print this message |
| -d,--msaDirectory <path> | build HLAGraph from gen and nuc MSAs provided by IMGT/HLA DB from given directory (required). Download a preformatted db from here |
| -o,--outfilePrefix <outfile> | use given outfile prefix for all output files (required) |
<outfileprefix>.result contains the typing result and the columns are:
1: Allele
2: #BasesMatched
3: Identity (#BasesMatched/MaxLen(query, db_allele))
4: Length of the assembled allele
5: Length of the matched allele from IMGT/HLA DB
<outfileprefix> contiains program log
Assembled allele sequences are outputed in files ending with .typed.fa.candiates (multi-FASTA format)
Dependecies can be easily downloaded by using Maven install command.
In each release, the pre-compiled jar is distributed with all necessary jars for dependencies, and they are:
- JGraphT 0.9.1 ( http://jgrapht.org/ )
- Apache Commons CLI 1.4 ( https://commons.apache.org/proper/commons-cli/ )
- fastutil 7.0.13 : Fast & compact type-specific collections for Java ( http://fastutil.di.unimi.it/ )