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MetaDemultiplex (optional)

Obtain non-barcoded sequencing reads.

meta_demultiplex()
Demultiplexing sequencing reads

MetaRef

Obtain target and filter genome sequences from NCBI nucleotide database and index using the Bowtie 2 or Subread aligner

download_refseq()
Download RefSeq genome libraries
mk_bowtie_index()
Make a Bowtie2 index
mk_subread_index()
Make a Subread index

MetaAlign

Align sequencing reads to indexed target genome sequences

align_target()
Align microbiome reads to a set of reference libraries
align_target_bowtie()
Align microbiome reads to set of indexed Bowtie2 libraries
align_details
A universal parameter settings object for Rsubread alignment
bt2_16S_params
A universal parameter object for Bowtie 2 16S alignment
bt2_regular_params
A universal parameter object for Bowtie 2 metagenomic or non-16S alignment
bt2_missing_params
A universal parameter object for Bowtie 2 metagenomic alignment where the host genome is thought to be absent from the reference database

MetaFilter

Remove reads mapped to indexed host genome sequences

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

MetaID

Reassign ambiguously mapped reads to probable source genome

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

MetaBLAST

BLAST assigned reads against the NCBI nucleotide database to check read identity.

metascope_blast()
Blast reads from MetaScope aligned files

MetaCombine

Aggregate samples into a MultiAssayExperiment compatible with the animalcules package

convert_animalcules()
Create a multi-assay experiment from MetaScope output for usage with animalcules
convert_animalcules_silva()
Create a multi-assay experiment from MetaScope output for usage with animalcules with the SILVA 13_8 database
convert_animalcules_patho()
Create a multi-assay experiment from PathoScope 2.0 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
blast_result_metrics()
Calculates result metrics from a blast results table
blastn_results()
rBlast_results
blastn_single_result()
blastn_single_result
check_blastn_exists()
Check if blastn exists on the system
get_seqs()
Gets sequences from bam file
taxid_to_name()
Converts NCBI taxonomy ID to scientific name