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ethill/ulana

By ethill

•Updated over 3 years ago

Bacterial genome assembly and annotation using ONT long read data

Image
0

1.1K

ethill/ulana repository overview

⁠Ulana

Unicellular Long-read Assembly aNd Annotation

A bacterial genome assembly and annotation pipeline using Fast, HAC or SUP ONT basecalled data from MinION and Flongle flow cells.

ulana

  1. vt. To plait, weave, knit, braid; plaiting, weaving. Also unala, nala, unana. Mea ulana ʻia, plaited or woven material, textile. Mea ulana lole, weaver (Isa. 38.12), loom. (PPN langa.)
 _   _ _
| | | | | __ _ _ __   __ _
| | | | |/ _` | '_ \ / _` |
| |_| | | (_| | | | | (_| |
 \___/|_|\__,_|_| |_|\__,_|


Ulana v1.0.2

Bacterial genome assembly and annotation
pipeline using Fast, HAC, or SUP ONT basecalled
data from MinION and Flongle flow cells

Usage: /usr/bin/ulana
  -h    help (prints this message)
  -v    version
  -q    minimum quality score; default is 10
  -l    minimum read length; default is 1000
  -c    number of cores to use; default is 4
  -i    name of input fastq file containing reads
  -b    type of basecalling used; the options are: r941_min_fast_g507, r941_min_hac_g507, r941_min_sup_g507

⁠Source code

Source code can be retrieved from Github (https://github.com/ehill-iolani/ulana⁠):

git clone https://github.com/ehill-iolani/Ulana.git

⁠Running the container

Start the Docker container as an interactive terminal and mount your data as a volume

⁠Sample commands

Fast basecalling

ulana -q 8 -l 1500 -c 56 -i fast_basecalled_reads.fastq -b r941_min_fast_g507

HAC basecalling

ulana -q 9 -l 1500 -c 56 -i hac_basecalled_reads.fastq -b r941_min_hac_g507

SUP basecalling

ulana -q 10 -l 1500 -c 56 -i sup_basecalled_reads.fastq -b r941_min_sup_g507

Tag summary

Content type

Image

Digest

sha256:c0a53ff58…

Size

5.1 GB

Last updated

over 3 years ago

docker pull ethill/ulana