Crate readfish_tools

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Readfish-tools

readfish-tools is a collection of utilities to provide a standardised way of analysing readfish runs that have been run. Currently the accepted analysable inputs are sequencing summary files, BAM of all produced FASTQ, and the TOML file that was used to configure the readfish run.

The intention is to demultiplex a bam/paf/sequencing summary into regions and barcodes then have methods to provide the summary stats for this function.

The crate is split into modules handling separate functionalities.

Modules

nanopore - Flowcell related functionality. channels - Channel Hashmaps for MinION and Flongle. paf - PAF related functionality. readfish - Readfish TOML related functionality. readfish_io - Custom functions and wrappers related IO functionality. sequencing_summary - Sequencing summary related functionality.

Modules

  • nanopore
    Flowcell and Condition utilities.
  • paf
    Paf file functions In this module we implement a Paf struct and functions to read and write Paf files. A lot of this was lifted from https://github.com/mrvollger/rustybam/blob/main/src/paf.rs
  • readfish
    Ports of readfish functions from python to rust. The functions are in order to parse a TOML file for configuring a readfish run, and implement all the same methods as the python version. This allows parsing the TOML Into the correct regions and barcodes, and then using the same methods to get the same results as readfish.

Structs

  • ConditionSummary
    Represents a summary of sequencing data, including various metrics related to the output of the experiment.
  • ContigSummary
    Represents a summary of a contig or sequence from a sequencing experiment. It includes various metrics related to the contig’s characteristics and read mapping.
  • MeanReadLengths
    Represents the mean read lengths for on-target, off-target, and total reads.
  • ReadfishSummary
    Organise the data and methods for analysing a readfish PAF file.
  • Summary
    A struct representing a summary of conditions.

Functions