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.
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