slow5lib

Note: This documentation is far from being complete and perfect. So if you need a new functionality, want to clarify something, find something is not right, facing a weird bug when using this API etc. do not hesitate to open an issue. Nowadays, bioinformatics tools written in C/C++ are getting fewer and fewer, so I would be glad to help.

NAME

slow5lib - slow5 Overview

DESCRIPTION

slow5lib is a library for reading and writing SLOW5 files. Compiling slow5lib requires a C compiler that conforms to at least c99 standard with X/Open 7, incorporating POSIX 2008 extension support.

Table of Contents

Data Structures

The slow5_file_t structure stores the file pointer, parsed SLOW5 header and other metadata of an opened SLOW5 file. The user can directly access the struct member slow5_hdr_t *header which contains the pointer to the parsed SLOW5 header. Other struct members are private and not supposed to be directly accessed.

The slow5_hdr_t structure stores a parsed SLOW5 header. This structure has the following form:

typedef struct {

    /* private struct members that are not supposed to be directly accessed are not shown.
       the order of the memebers in this struct can subject to change.
    */

    struct slow5_version version;       // SLOW5 file version
    uint32_t num_read_groups;           // Number of read groups

} slow5_hdr_t;

The slow5_version structure contains the major, minor and patch version as follows:

struct slow5_version {
    uint8_t major;  // major version
    uint8_t minor;  // minor version
    uint8_t patch;  // patch version
};

The slow5_rec_t structure stores a parsed slow5 record. This structure has the following form:

typedef struct {
    slow5_rid_len_t read_id_len;        // length of the read ID string (does not include null character)
    char* read_id;                      // the read ID
    uint32_t read_group;                // the read group
    double digitisation;                // the number of quantisation levels - required to convert the signal to pico ampere
    double offset;                      // offset value - required to convert the signal to pico ampere
    double range;                       // range value - required to convert to pico ampere
    double sampling_rate;               // the sampling rate at which the signal was acquired
    uint64_t len_raw_signal;            // length of the raw signal array
    int16_t* raw_signal;                // the actual raw signal array

    /* Other private members for storing auxilliary field which are not to be directly accessed*/

} slow5_rec_t;

High-level API

High-level API consists of following functions:

Common

Reading

Writing

You may also refer to examples here.

Low-level API for reading and writing SLOW5 files

Low-level API allows much more efficient access to BLOW5 files compared to the high-level API. Low-level API is documented here.

Easy multi-thread API

The easy multi-thread (called mt API) API allows the user to access SLOW5 using multiple threads, simply by specifying the number of threads, rather than needing to write their own multi-threading code. mt API is documented here. Note that this API is for your convenience, rather than for efficiency.

CITATION

Please cite the following in your publications when using slow5lib/pyslow5:

Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40, 1026-1029 (2022). https://doi.org/10.1038/s41587-021-01147-4

@article{gamaarachchi2022fast,
  title={Fast nanopore sequencing data analysis with SLOW5},
  author={Gamaarachchi, Hasindu and Samarakoon, Hiruna and Jenner, Sasha P and Ferguson, James M and Amos, Timothy G and Hammond, Jillian M and Saadat, Hassaan and Smith, Martin A and Parameswaran, Sri and Deveson, Ira W},
  journal={Nature biotechnology},
  pages={1--4},
  year={2022},
  publisher={Nature Publishing Group}
}