Eisenia

A package for kmer-based probablistic graph genome assembly and analysis

WIP

How to turn the package into a runnable executable from the command line

echo 'export PATH="$HOME/Desktop/Microbes/Eisenia/bin:$PATH"'

mkdir data
wget --directory-prefix data/ ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/Escherichia_virus_phiX174/latest_assembly_versions/GCF_000819615.1_ViralProj14015/GCF_000819615.1_ViralProj14015_genomic.fna.gz

Making a package

julia> using Pkg

julia> Pkg.generate("Eisenia")
Generating project Eisenia:
    Eisenia/Project.toml
    Eisenia/src/Eisenia.jl
Dict{String,Base.UUID} with 1 entry:
  "Eisenia" => UUID("ff91eec8-cf20-4569-aeea-763e189e8d12")
# move all of my code into it
(v1.2) pkg> activate .
Activating environment at `~/Repos/Eisenia/Project.toml`

# add things

developing packages outside of the standard Julia locations

mkdir ~/.julia/config
echo 'push!(LOAD_PATH, expanduser("~/Repos/Eisenia/src"))' > ~/.julia/config/startup.jl

config file = fastq files -> [group]
if no group provided then everything is the same group

every fastq file is counted at 7, 11, 13, 17, ... primes until linear r squared detected
assess how this varies depending on error rate, do we need to exclude kmers with counts < 2? That's the quickest way to remove errors

take kmer list and initialize graph nodes

read through reads and build edges

read through reads and return most likely reads

reads > kmers
kmers > graph nodes
graph nodes + reads > edges
nodes + edges + reads > maximum likelihood reads

repeat until convergence

use graph + reads for error correction

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1554-6