malaria-profiler

Install

# Run the following depending on your platorm

# linux
wget  https://raw.githubusercontent.com/jodyphelan/malaria-profiler/main/conda/linux.env.txt
conda create --name malaria-profiler --file linux.env.txt

# macos
wget  https://raw.githubusercontent.com/jodyphelan/malaria-profiler/main/conda/macos.env.txt
conda create --name malaria-profiler --file macos.env.txt

# Then the following commands on all platforms
conda activate malaria-profiler
pip install git+https://github.com/jodyphelan/malaria-profiler.git
pip install git+https://github.com/jodyphelan/pathogen-profiler.git
malaria-profiler update_db

Updating

conda activate malaria-profiler
pip install --force-reinstall git+https://github.com/jodyphelan/malaria-profiler.git
pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git

Usage

Input types

Malaria-Profiler species prediciton is currently available to run on a fastq, bam, cram, fasta or vcf data. The output is a txt file with the species prediction and if there is a resistance database then it will also output a list of variants and if they have been associated with drug resistance.

Fastq data

Raw sequencing data in fastq format can been used as input using the following command. The second read is optional.

malaria-profiler profile -1 </path/to/reads_1.fq.gz> -2 </path/to/reads_2.fq.gz> -p <sample_name> -t [threads] --txt 

Bam/Cram

Aligned data in the form of bam or cram files can be used. Please note that the alignment files must have been generated with the same reference genome (even the chromosome names) as those used by malaria-profiler database.

malaria-profiler -a </path/to/bam/cram> -p <sample_name> -t [threads] --txt

Fasta

Assembled genomes or gene sequencves in fasta format can been used as input using the following command.

malaria-profiler -f </path/to/fasta> -p <sample_name> -t [threads] --txt

VCF

Varaints stored in VCF format can been used as input using the following command. Again the chromosome names must match those in the species-specific database.

malaria-profiler -v </path/to/vcf> -p <sample_name> -t [threads] --txt

General options

If you have used a reference genome with different sequence names that you have used to generate a bam/cram/vcf then it is possible to align the malaria-profiler databases to use the same sequence names. Please go to the custom databases section to find out more.

Other useful options arguments include

• --threads - sets the number of parallel threads
• --platform - sets the platform that was used to generate the data (default=illumina)
• --txt - outputs a text based report

A full list of arguments can be found by running malaria-profiler profile -h

Collating results across runs

The results from numerous runs can be collated into one table using the following command.

malaria-profiler collate 

How it works?

Species prediction

Species prediction is performed by looking for pre-detemined kmers in read files which belong to a specific species. If no species is found using this method, mash is run using a database of all Plasmodium mitochondrial sequences from GTDB to find the top 10 closest genomes.

Resistance prediction

Resistance prediction is performed by aligning the read data to a species-specific reference genome and looking for resistance associated genes and variants. The reference and resistance database is stored in the malaria-db github repo. At the moment resistance prediction is available for:

• Plasmodium falciparum

If you would like to suggest another organism please leave a comment in this thread.