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Reference Genome Library

Start here to download reference genomes for processing.

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