Haplotype-Lso is a program for the automated determination of C. liberibacter solanacearum. For the input, it takes capillary sequencing data from 16S, 16S-23S, and 50S locus enrichment. It then performs a multi-locus sequence typing (MLST) following IPPC (International Plant Protection Convention) standard DP 21: Candidatus Liberibacter solanacearum.


The Haplotype-Lso start page.

Public Web App

You can find the publically available version at https://haplotype-los.bihealth.org (hosting is provided by Core Unit Bioinformatics of the Berlin Institute of Health). To get started, you can follow the Haplotype-Lso Tutorial.

Running on your Computer

Haplotype-Lso has very low hardware requirements but depends on several external programs (e.g., NCBI BLAST) and must be run on a Linux computer. The easiest way is to install it via Docker:

$ docker run quay.io/biocontainers/haplotype-lso:<version>

# for example:

$ docker run quay.io/biocontainers/haplotype-lso:0.3.2--0

See here for a list of all versions.

You can also install it via Bioconda. After installing Bioconda:

$ conda install haplotype-lso

Source Code / Open Source

Haplotype-Lso is written in the Python programming language using Plotly Dash. It is licensed under the permissive MIT license and you can find the source code in the Github project.

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