Function reference • MetaScope

Reference Genome Library

Start here to download reference genomes for processing.

taxonomy_table: Taxonomy table

download_refseq(): Download RefSeq genome libraries

Demultiplex

Preprocessing for 16S data.

demultiplex(): Demultiplexing sequencing reads

Index Creation

Create compatible indexes from downloaded reference genomes.

mk_bowtie_index(): Make a Bowtie2 index

mk_subread_index(): Make a Subread index

Alignment with Reference Libraries

Mapping sequencing reads to the target & filter libraries.

align_target(): Align microbiome reads to a set of reference libraries

filter_host(): Use Rsubread to align reads against one or more filter libraries and subsequently remove mapped reads

align_details: A universal parameter settings object for Rsubread alignment

align_target_bowtie(): Align microbiome reads to set of indexed Bowtie2 libraries

filter_host_bowtie(): Use Rbowtie2 to align reads against one or more filter libraries and subsequently remove mapped reads

bt2_16S_params: A universal parameter object for Bowtie 2 16S alignment

bt2_loose_params: A universal parameter object for Bowtie 2 loose alignment

Genome Identification

Identify which genomes are most likely to be represented in the sample.

metascope_id(): Identify which genomes are represented in a processed sample

Downstream Analysis with animalcules

Convert MetaScope output to be compatible with the animalcules R package.

convert_animalcules(): Create a multi-assay experiment from MetaScope output for usage with animalcules

Helper Functions

These functions were developed to aid in carrying out other primary functions.

remove_matches(): Helper function to remove reads matched to filter libraries

combined_header(): Create a combined .bam header

bam_reheader_R(): Replace the header from a .bam file

get_children(): Get child nodes from NCBI taxonomy

merge_bam_files(): Merge multiple .bam files

count_matches(): Count the number of base lengths in a CIGAR string for a given operation

extract_reads(): Helper function for demultiplexing

locations(): Helper Function for MetaScope ID

filter_unmapped_reads(): Filter unmapped reads

check_samtools_exists(): Check if samtools exists on the system