a-wtdbg2

accelerated wtdbg2, which is based on the de novo assembler wtdbg2 on https://github.com/ruanjue/wtdbg2

Experiment Setup

CPU: 2 Intel Xeon E5-2680v4 CPUs,each with 14 hyper-threaded cores.

Memory: 256GB

Operation System: Red Hat 7.2

Compiler: gcc 4.8.3

Datasets

All the different command lines of various datasets have already been integrated in run.sh, here only the download links are presented.

E.coli: http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz

C.elegans: https://github.com/PacificBiosciences/DevNet/wiki/C.-elegans-data-set

D. melanogaster ISO1: https://www.ebi.ac.uk/ena/data/view/SRR6702603

Human NA24385: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb/

Human HG00733: https://www.ebi.ac.uk/ena/data/view/SRR7615963

Installation of a-wtdbg2

To compile and install the a-wtdbg2, please use make and make install.

cd a-wtdbg2
make
make install

Running a-wtdbg2

The command lines for assembly and subsequent consensus which is used for assessment by Quast is in run.sh, thus to run a-wtdbg2, please directly run run.sh.

./run.sh