construct_contigs: Construct contigs from read clusters

In ctl43/TranSpotteR: Pipeline for identifying LINE1 insertoin in the WGS data

Construct contigs from read clusters

Description

Perform Overlap-Layout-Consensus (OLC) to combine reads from cluster into a contigs.

Usage

construct_contigs(x, BPPARAM = MulticoreParam(workers = 10))

Arguments

x	A GRanges object generated from cluster_reads.
BPPARAM	A BiocParallelParam object controlling parameters in parallelization.

Details

In the first round of assembly, reads consisting the clusters and their partner reads are assembled separately. In the second round of assembly, the cluster contigs and their partners contigs are assembled to create a longer contig. In every assembly step, more than one contigs can be constructed. If no longer contig is formed, the cluster contigs and partner contigs are remained. On the other hand, if a longer contig is formed, the cluster and partner contig are erased even the contigs do not involve in the composition of the longer contig. The number of reads used in constructing each contig are also recorded.

Value

A GRange object with a DataFrame that contains reads consisting the cluster, their partner reads, contigs assembled from cluster reads (cluster_contigs), contigs assembled from partner reads (partner_contigs) and contig combining cluster and partner contig (long_contigs). The number of reads used in constructing each contig are recorded in the elementMetadata of the contigs.

Author(s)

Cheuk-Ting Law

See Also

construct_contigs

ctl43/TranSpotteR documentation built on Sept. 9, 2022, 5:49 p.m.