Oxford nanopore

[danejo3]

The purpose of this PR is to introduce support for Oxford Nanopore reads.

To differentiate between the two types of long reads: Pacbio and Oxford (and it's various subkinds such as the older Pacbio reads (not hifi)), users will need to provide the read type for each sample in the config file.

The following read types can be passed into YEAT with their assembly algorithms.

Readtype	Algorithm
paired	Spades, Megahit, Unicycler
pacbio-raw	Flye, Canu
pacbio-corr	Flye, Canu
pacbio-hifi	Flye, Canu
nano-raw	Flye, Canu
nano-corr	Flye, Canu
nano-hq	Flye, Canu

Example config file:

  "samples": {
      "sample1": {
          "paired": [
              "yeat/tests/data/short_reads_1.fastq.gz",
              "yeat/tests/data/short_reads_2.fastq.gz"
          ]
      },
      "sample2": {
          "paired": [
              "yeat/tests/data/Animal_289_R1.fastq.gz",
              "yeat/tests/data/Animal_289_R2.fastq.gz"
          ]
      },
      "sample3": {
          "pacbio-hifi": [
              "yeat/tests/data/ecoli.fastq.gz"
          ]
      },
      "sample4": {
          "nano-hq": [
              "yeat/tests/data/ecolk12mg1655_R10_3_guppy_345_HAC.fastq.gz"
          ]
      }
  }

Users can now assemble Oxford reads with canu and Flye. Users can also assemble old non-hifi pacbio reads with canu and Flye as well.