Rsubread (version 1.22.2)

buildindex: Build index for a reference genome

Description

An index needs to be built before read mapping can be performed. This function creates a hash table for the reference genome, which can then be used by Subread and Subjunc aligners for read alignment.

Usage

buildindex(basename,reference,gappedIndex=TRUE,indexSplit=TRUE,memory=8000,
TH_subread=100,colorspace=FALSE)

Arguments

basename

character string giving the basename of created index files.

reference

charater string giving the name of the file containing all the refernece sequences.

gappedIndex

logical. If FALSE, 16mers (subreads) will be extracted from every chromosomal location of a reference genome and then they will be used to build a hash table index. By default(TRUE), subreads are extracted in every three bases from the genome.

indexSplit

logical. If TRUE, the built index is allowed to be splitted into multiple segments. The number of such segments is determined by memory value, genome size and permitting of gaps between subreads(gappedIndex). If indexSplit is set to FALSE, a single-segment index (no splitting) will be generated regardless of what value is chosen for memory.

memory

numeric value specifying the amount of memory to be requested in megabytes. 8000 MB by default.

TH_subread

numeric value specifying the threshold for removing highly repetitive subreads (16bp mers). 100 by default. Subreads will be excluded from the index if they occur more than threshold number of times in the genome.

colorspace

logical. If TRUE, a color space index will be built. Otherwise, a base space index will be built.

Value

No value is produced but index files are written to the current working directory.

Details

This function generates a hash table (an index) for a reference genome, in which keys are subreads (16mers) and values are their chromosomal locations in the reference genome. By default, subreads will be extracted in every three bases from a reference genome. However, if gappedIndex is set to FALSE, then subreads will be extracted from every chromosomal location of genome for index building. The built index can then be used by Subread (align) and subjunc aligners to map reads(Liao et al. 2013).

Highly repetitive subreads (or uninformative subreads) are excluded from the hash table so as to reduce mapping ambiguity. TH_subread specifies the maximal number of times a subread is allowed to occur in the reference genome to be included in hash table.

The built index might be splitted into multiple segments if its size is greater than memory value. The number of such segments is dependent on memory value, size of reference genome and whether gaps are allowed between subreads extracted from genome. Only one segment is loaded into memory at any time when read alignment is being carried out. The larger the memory value, the faster the read mapping will be. If indexSplit is set to FALSE, the index will not be splitted and this will enable maximum mapping speed to be achieved.

The index needs to be built only once and it can then be re-used in the subsequent alignments.

References

Yang Liao, Gordon K Smyth and Wei Shi. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013.

Examples

# Build an index for the artifical sequence included in file 'reference.fa'
library(Rsubread)
ref <- system.file("extdata","reference.fa",package="Rsubread")
buildindex(basename="./reference_index",reference=ref)