sublong {Rsubread} | R Documentation

## Align Long Sequence Reads to a Reference Genome via Seed-and-Vote

### Description

This function aligns DNA-seq reads, generated by long-read sequencing technologies such as Nanopore and PacBio sequencers, to a reference genome.

### Usage

    sublong(

        # basic input/output options
        index,
        readFiles,
        outputFiles,
        outputFormat = "BAM",
        nthreads = 1)

### Arguments

`index` | a character vector giving the basename of index files. Index files should be located in the current directory. The provided index should be a full index and also it should have only one block. See `buildindex` for index building options.
`readFiles` | a character vector giving the names of input files that contain long sequence reads. FASTQ and gzipped FASTQ formats are both accepted.
`outputFiles` | a character vector specifying the names of output files that contain read mapping results.
`outputFormat` | a character string specifying the format of output files. `BAM` by default. Acceptable formats include `SAM` and `BAM`.
`nthreads` | an integer giving the number of threads used for mapping. `1` by default. Note that when more than one thread is used, the order of reads might be changed in the output.

### Details

`sublong` is designed for the mapping of long reads. It performs full alignment of reads by performing seed-and-vote mapping followed by a bounded dynamic programming procedure. `sublong` is able to map reads as long as millions of bases.

`sublong` is extremely fast. It takes less than 10 minutes to complete the mapping of more than 100,000 long reads generated from Nanopore MinION ultra-long sequencing protocol.

The number of CIGAR operations (eg. insertion and deletion) reported for a long read may exceed the limit on the total number of operations allowed in a CIGAR string (up to 65,535 operations in a CIGAR string in BAM output and up to 99,900 operations in a CIGAR string in SAM output). If this limited is exceeded, the read will be soft clipped.

### Author(s)

Yang Liao and Wei Shi

### Examples

    ref <- system.file("extdata","reference.fa",package="Rsubread")
    buildindex(basename="./full_index",reference=ref,gappedIndex=FALSE, indexSplit=FALSE)
    reads <- system.file("extdata","longreads.txt.gz",package="Rsubread")
    sublong("./full_index",reads,"./Long_alignment.BAM",nthreads=4)

[Package Rsubread version 2.8.2 Index]