GloTK is the Genomes of Luminous Organisms Toolkit. It contains scripts to facilitate genome assembly optomization and analysis using common genome assemblers.
Currently there are only scripts for one assembler:
- Meraculous 188.8.131.52+
mer_reporter.pyscript currently requires the following to be installed:
You can install the
gloTK package on your linux machine by typing
pip install gloTK in your terminal.
Major releases of
gloTK are uploaded to the Python Package Index.
To use these programs, install
gloTK as described above and type
your terminal. If you hit the
tab key a few times your computer should try to
autocomplete and you will see a few options:
- Generates HTML reports of all Meraculous assemblies found within
the current working directory (CWD). Collates all relevant files and images
meraculous_reportsdirectory in the CWD.
- Generates HTML reports of all Meraculous assemblies found within the current working directory (CWD). Collates all relevant files and images into a
- This allows the user to input a single meraculous config file, and to define
parameters to sweep on and optomize. Currently this program supports sweeping
glotk-sweepinto your terminal after installing will give you more details.
- This allows the user to input a single meraculous config file, and to define parameters to sweep on and optomize. Currently this program supports sweeping on
v0.1.15 - 20161116
- This version incorporates glotk-project. This script reads in a config file and generates a 'glotk_project' directory in which information about the libraries, assemblies, et cetera for this Meraculous genome project is stored. Assemblies, reports, config files, et cetera will take place in adjacent directories
- gloTK project files will now take on the following file structure:
project_dir/ |--glotk_info/ | | default_config.config | | sample_metadata.config | | read_metadata.config | | assemblynumber_to_runname.txt | | | |--activity_log/ | | as000.log | | as001.log | | etcetera.log | | | |--read_configs/ | reads0.yaml #this is the initial yaml file for imported reads | reads1.yaml #reads generated from Seqprep, trimmomatic, et cetera | |--glotk_assemblies | |--as000_<assembly_name>/ | | |--assembler_output/ | | | |--as001_20161102_ME_pleu_bach_k63_d1/ | |--meraculous_etcetera | |--glotk_configs | as000_<assembly_name>.config | as001_20161102_ME_pleu_bach_k63_d1.config | |--glotk_reads | | reads.log | | | |--reads0/ | | <forward_reads_symlink>.fq.gz | | <reverse_reads_symlink>.fq.gz | | | |--reads1/ | <processed_forward>.fq.gz | <processed_reverse>.fq.gz | |--glotk_fastqc |--glotk_kmers |--glotk_reports
v0.1.14 - 20161102
- Gave a --triplet flag to glotk-sweep to cause the assembler to run diploid modes 0, 1, and 2 on the same kmer size.
v0.1.13 - 20161102
- Made glotk-sweep function by inputting each value of k to assemble for, rather than using 'sweep start', 'sweep stop', and 'sweep interval'. Usage is: '--slist 23 27 57' to perform assemblies for those three values