Metaphlan

Introduction

Metaphlan is computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.

Versions

• 4.0.2

• 4.0.6

Commands

• add_metadata_tree.py

• aggregate_scores_in_intervals.py

• align_print_template.py

• axt_extract_ranges.py

• axt_to_fasta.py

• axt_to_lav.py

• axt_to_maf.py

• bed_bigwig_profile.py

• bed_build_windows.py

• bed_complement.py

• bed_count_by_interval.py

• bed_count_overlapping.py

• bed_coverage_by_interval.py

• bed_coverage.py

• bed_diff_basewise_summary.py

• bed_extend_to.py

• bed_intersect_basewise.py

• bed_intersect.py

• bed_merge_overlapping.py

• bed_rand_intersect.py

• bed_subtract_basewise.py

• bnMapper.py

• bowtie2

• bowtie2-build

• breadth_depth.py

• cleanup-blastdb-volumes.py

• consensus_aDNA.py

• consensus.py

• div_snp_table_chr.py

• extract_markers.py

• find_in_sorted_file.py

• gene_fourfold_sites.py

• get_scores_in_intervals.py

• interval_count_intersections.py

• interval_join.py

• int_seqs_to_char_strings.py

• lav_to_axt.py

• lav_to_maf.py

• line_select.py

• lzop_build_offset_table.py

• maf_build_index.py

• maf_chop.py

• maf_chunk.py

• maf_col_counts_all.py

• maf_col_counts.py

• maf_count.py

• maf_covered_ranges.py

• maf_covered_regions.py

• maf_div_sites.py

• maf_drop_overlapping.py

• maf_extract_chrom_ranges.py

• maf_extract_ranges_indexed.py

• maf_extract_ranges.py

• maf_filter_max_wc.py

• maf_filter.py

• maf_gap_frequency.py

• maf_gc_content.py

• maf_interval_alignibility.py

• maf_limit_to_species.py

• maf_mapping_word_frequency.py

• maf_mask_cpg.py

• maf_mean_length_ungapped_piece.py

• maf_percent_columns_matching.py

• maf_percent_identity.py

• maf_print_chroms.py

• maf_print_scores.py

• maf_randomize.py

• maf_region_coverage_by_src.py

• maf_select.py

• maf_shuffle_columns.py

• maf_species_in_all_files.py

• maf_split_by_src.py

• maf_thread_for_species.py

• maf_tile_2bit.py

• maf_tile_2.py

• maf_tile.py

• maf_to_axt.py

• maf_to_concat_fasta.py

• maf_to_fasta.py

• maf_to_int_seqs.py

• maf_translate_chars.py

• maf_truncate.py

• maf_word_frequency.py

• mask_quality.py

• merge_metaphlan_tables.py

• metaphlan

• mMK_bitset.py

• nib_chrom_intervals_to_fasta.py

• nib_intervals_to_fasta.py

• nib_length.py

• one_field_per_line.py

• out_to_chain.py

• plot_tree_graphlan.py

• polymut.py

• poly.py

• prefix_lines.py

• pretty_table.py

• qv_to_bqv.py

• random_lines.py

• read_fastx.py

• sample2markers.py

• strainphlan

• strain_transmission.py

• sumlabels.py

• sumtrees.py

• table_add_column.py

• table_filter.py

• tfloc_summary.py

• ucsc_gene_table_to_intervals.py

• wiggle_to_array_tree.py

• wiggle_to_binned_array.py

• wiggle_to_chr_binned_array.py

• wiggle_to_simple.py

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=metaphlan   # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load metaphlan/XXXX     ### Latest version is recommended.