/pima

Plasmid and antimicrobial resistance pipeline

Primary LanguagePython

pima

Plasmid and antimicrobial resistance pipeline

Example Installation

Pima is not yet packaged, but its primary dependencies are mostly available. guppy must be manually installed with info here. If you don't yet have conda installed you'll need to do that here. Once installed you can create an environment where pima.py will run.

conda create -n pima_env2 python=2.7.16
source activate pima_env2
# install python modules
conda install -c conda-forge joblib numpy pandas pathos -y
# install bioinfx packages
conda install -c bioconda bcftools bedtools blast flye mummer medaka miniasm minimap2 nanopolish parallel porechop qcat racon samtools spades wtdbg -y
git clone https://github.com/abconley/pima.git $HOME
python ~/pima/pima.py --help
Compatibility

Currently several unix utilities are used, so this is not compatible with Windows OS. CentOS and Ubuntu are both known working OSes.

Dependencies
System Command Package
bcftools BCFtools
bedtools BEDTools
blastn BLAST+
dnadiff MUMmer
faidx SAMtools
flye Flye
parallel GNU parallel
guppy_basecaller Guppy
makeblastdb BLAST+
medaka_consensus Medaka
miniasm miniasm
minimap2 minimap2
nanopolish Nanopolish
nanopolish_makerange.py Nanopolish
pblat pblat
pChunks.R local R script
porechop Porechop
qcat Qcat
racon racon
read_fast5_basecaller.py Guppy
samtools SAMtools
spades.py SPAdes
wtdbg2 Wtdbg2
wtpoa-cns Wtdbg2
awk Unix
cat Unix
grep Unix
head Unix
ls Unix
sed Unix
sort Unix

Literature Citations