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StrainFLAIR minimal example cookbook

Prerequisite

Datasets for this cookbook are available in the folder data/minimal_example/. It contains 4 complete genomes (fasta files) and a mixture of simulated reads with 0.001% of errors composed of 67% of reads from D4 and 33% of reads from LM33 (fastq file).

Full commands: The full commands are proposed at the end of the section.

Computation time is approximately 3 minutes for the indexation step, 3 minutes for the mapping step and 1 minute for the query step.

Consider 4 reference genomes:

First, create a file of file (fof) used as input for StrainFLAIR. Each line of the input fof contains exactly one fasta name. We may create this fof as follows:

ls data/minimal_example/*.fasta > data/list_fasta_min.txt

Second, run StrainFLAIR indexation step, using the input fof:

./StrainFLAIR.sh index -i data/list_fasta_min.txt -o myproject

The reference graph and its associated additionnal files have been created in the new directory myproject.

Third, query the variation graph by mapping any reads on it. Reads can be compressed in a fastq.gz format.

./StrainFLAIR.sh query -g myproject/graphs/all_graphs -f1 data/minimal_example/mixture_D4_LM33_67_33.fastq -t 24 -p myproject/graphs/dict_clusters.pickle -d myproject -o minimalexample

That's it! Mapping files are available in mapping/, and abundance tables are available in results/.

The final result is a csv table containing each reference genome in line identified by their accession number. Columns contained the proportion of detected genes and the estimated strain-level abundance according to different computation methods. Here we found the initial ratio of around 65-68% for D4 (CP010143.1) and around 31-35% for LM33 (NZ_LN874954.1).

Here is a small example:

,detected_genes,mean_abund,mean_abund_nz,median_abund,median_abund_nz
NZ_LN874954.1,0.9774620284174425,31.897899712576486,34.90845134147716,31.76353773804796,34.8974830123928
CP014492.1,0.21266968325791855,0.0,0.0,0.0,0.0
CP010143.1,0.9890345649582837,68.10210028742353,65.09154865852284,68.23646226195204,65.10251698760719
AP022815.1,0.07082211638020294,0.0,0.0,0.0,0.0

Full commands:

ls data/minimal_example/*.fasta > data/list_fasta_min.txt
./StrainFLAIR.sh index -i data/list_fasta_min.txt -o myproject
./StrainFLAIR.sh query -g myproject/graphs/all_graphs -f1 data/minimal_example/mixture_D4_LM33_67_33.fastq -t 24 -p myproject/graphs/dict_clusters.pickle -d myproject -o minimalexample