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biom summarize_folder.sh
Usage:
biom-summarize_folder.sh <folder path>
For a given input folder, this script will attempt to summarize all biom-formatted OTU tables (extension .biom) contained therein. Output files will be named just as the input tables but with a ".summary" extension. It will skip any tables that have already been summarized.
Script wiki pages:
akutils
akutils align_and_tree
akutils check
akutils check_result
akutils configure
akutils core diversity
akutils format_database
akutils join_paired_reads
akutils phix_filtering
akutils pick_otus
akutils primer_file
akutils primer_list
akutils print_config
akutils strip_primers
akutils test
akutils test_result
akutils update
ancomR.sh
biom-summarize_folder.sh
biomtotxt.sh
concatenate_fastqs.sh
convert_table_for_ancomR.sh
fastq_data.sh
fasta_length_histogram.sh
fastq_length_histogram.sh
filter_fasta_by_length.sh
filter_fastq_by_length.sh
filter_observations_by_sample.sh
indicator_species.sh
ITSx_parallel.sh
mapcats.sh
preprocess_otus_for_ghost-tree.sh
slurm_builder.sh
synthetic_index.sh
two-way_permanova.sh
txttobiom.sh
unwrap_fasta.sh
Tutorial pages:
akutils tutorial
ITS analysis
slurm usage
Running akutils on monsoon
Example: 2x300, 2 loci
akutils wiki home:
akutils wiki home
akutils home page:
akutils home page
akutils github page:
akutils github page