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Metagenome analysis of infant gut metagenomes - part 4

MetaPhlAn2

We will use only R1 reads for the following analyses.

#!/bin/bash -l
#SBATCH -J metaphlan2
#SBATCH -o metaphlan2_out_%A_%a.txt
#SBATCH -e metaphlan2_err_%A_%a.txt
#SBATCH -t 2:00:00
#SBATCH --mem=10000
#SBATCH --array=1-10
#SBATCH -n 1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH -p serial

module load biokit
mkdir /wrk/$USER/Metagenomics2019/Metaphlan2
cd /wrk/$USER/Metagenomics2019/Metaphlan2
name=$(sed -n "$SLURM_ARRAY_TASK_ID"p ../sample_names.txt)
metaphlan2.py ../trimmed_data/$name"_R1_trimmed.fastq" \
              --input_type fastq --nproc  $SLURM_CPUS_PER_TASK \
              --mpa_pkl /appl/bio/metaphlan/db_v20/mpa_v20_m200.pkl \
              --bowtie2db /appl/bio/metaphlan/db_v20/mpa_v20_m200 \
              --bowtie2out $name".bowtie2.bz2" \
              -o $name"_metaphlan.txt"

Merge the metaphlan2 outputs

module load biokit
merge_metaphlan_tables.py *_metaphlan.txt > infants_merged_table.txt
module purge

Optional

Make a heatmap from species level results.

module load bioconda/3
source activate metaphlan_plot_env
grep -E "(s__)|(^ID)" infants_merged_table.txt | grep -v "t__" | sed 's/^.*s__//g' > infants_metaphlan_species.txt

hclust2.py -i infants_metaphlan_species.txt -o infants_heatmap_species.png --ftop 25 \
            --f_dist_f braycurtis --s_dist_f braycurtis --cell_aspect_ratio 0.5 \
            -l --flabel_size 6 --slabel_size 6 --max_flabel_len 100 \
            --max_slabel_len 100 --minv 0.1 --dpi 300

GraPhlAn

export2graphlan.py --skip_rows 1,2 -i infants_merged_table.txt --tree infants.tree.txt \
                   --annotation infants.annot.txt --most_abundant 100 \
                    --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 \
                    --external_annotations 7 --min_clade_size 1

graphlan_annotate.py --annot infants.annot.txt infants.tree.txt infants.abundance.xml
graphlan.py --dpi 300 infants.abundance.xml infants.abundance.png --external_legends

StrainPhlAn

Follow the instructions for StrainPhlAn.
You need to decide the strain based on the MetaPhlAn2 results.