The scripts and classes are tested using Anaconda installation of python 3.5, Requires NEWBLER2.9 installed on system.
/your/project/root/directory
└── out
├── newbler
│ └── K0000X
│ └── input
│ └── K0000X.1.fq (binned reads from Diamond+blast2lca)
│ └── K0000X.2.fq (binned reads from Diamond+blast2lca)
├── pileup
│ └── K0000X
│ └── input
│ └── K0000X-contig00001
│ └── K0000X-contig00002
├── preNewbler
│ └── K0000X
│ └── K0000X (fastQ file)
├── pAss01
├── pAss03
├── pAss05
├── pAss10
└── pAss11
docker pull etheleon/python3
Run interactively
cd $projectFolder
docker run --rm -u 507 -v $PWD:/w -w /w -it etheleon/python3:0.1 /bin/bash
Much of the gene centric pipeline is only are scripts. pASS is just one part of this.
Classes
-
Newbler
- Newbler.geneCentricAssembly - runs Newbler2.9 assembler on a KO by KO basis, generating contigs for use later for pAss
- Newbler.mdrCentricAssembly - runs Newbler2.9 assembler on a KO by KO basis, but only for READs found in the MDR region, generating contigs for use later for pAss
-
Alignment Alignment.doPile - Generates a short read pileup for each of the contigs to be used later for assembly.
pileup