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Hierarchical (ABxCB) binning on metagenomic samples

Source: R/hierarchical_binning.R
hierarchical_binning.Rd

This function performs hierarchical binning on metagenomic samples, directly from FASTA or FASTQ files. First it analyzes sequences by long kmer analysis (k>8), as in abundance_based_binning. Then for each AB bin, it guesses the number of composition bins in it and performs composition based binning by short kmer analysis (k<8), as in composition_based_binning. See doi:10.1186/s12859-016-1186-3 for more details.

Usage

hierarchical_binning(
  ...,
  eMin = 1,
  eMax = 0,
  kMerSizeAB = 10,
  kMerSizeCB = 4,
  genomeSize = 3e+06,
  numOfClustersAB = 3,
  outputC = "ABxCB.cluster",
  keepQuality = FALSE,
  dryRun = FALSE,
  gzip = FALSE,
  numOfThreads = BiocParallel::bpworkers()
)

Arguments

...

Input sequences. Either character paths to FASTA/FASTQ files (uncompressed or gzip compressed), a DNAStringSet / QualityScaledDNAStringSet, or a ShortReadQ object. Non-file inputs are staged to a temporary FASTA/FASTQ file for the Java backend.

eMin

Exclude kmers of less or equal count.

eMax

Exclude kmers of more or equal count.

kMerSizeAB

kmer length for Abundance based Binning.

kMerSizeCB

kmer length for Composition based Binning.

genomeSize

Average genome size of taxa in the metagenome data.

numOfClustersAB

Number of Clusters for Abundance based Binning.

outputC

Output Hierarchical Binning (ABxCB) Clusters files location and prefix.

keepQuality

Keep fastq qualities on the output files. (will produce .fastq)

dryRun

Don't write any output files.

gzip

Gzip output files.

numOfThreads

Number of threads to use. Defaults to bpworkers().

Value

A MetabinResult object. Its assignments slot is a DataFrame:

  • read_id : read identifier from fasta header

  • ABxCB : read was assigned to this ABxCB cluster index

  • ABxCB.n : read to cluster ABxCB.n distance

For backwards-compatible data.frame output use as.data.frame(result).

References

https://github.com/gkanogiannis/metabinR

Author

Anestis Gkanogiannis, anestis@gkanogiannis.com

Examples

res <- hierarchical_binning(
    system.file("extdata", "reads.metagenome.fasta.gz", package = "metabinR"),
    dryRun = TRUE, kMerSizeAB = 4, kMerSizeCB = 2
)
res
#> MetabinResult (ABxCB)
#>   reads:     26,664
#>   clusters:  1
#>   inputs:    1 file(s)
#>     - /home/runner/work/_temp/Library/metabinR/extdata/reads.metagenome.fasta.gz