Parallel assembly algorithm building on top of IDBA.
#Instructions
Get idba from either https://github.com/loneknightpy/idba or http://hku-idba.googlecode.com/files/idba-1.1.1.tar.gz
To build the ScalaDBG_SP version:
cp scaladbg_sp_ud.cpp idba/src/release/idba_ud.cpp
cd idba/
# Now change build.sh: Change the line with ./configure to: ./configure CXX=mpic++ CXXFLAGS=-lrt
./build.sh
#./configure CXX=mpic++ CXXFLAGS=-lrt
To build the ScalaDBG_PP version:
cp scaladbg_pp_ud.cpp idba/src/release/idba_ud.cpp
cd idba/
# Now change build.sh: Change the line with ./configure to: ./configure CXX=mpic++ CXXFLAGS=-lrt
./build.sh
./configure CXX=mpic++ CXXFLAGS=-lrt
The binary to use is idba_ud
Datasets were retrieved from the following: Ecoli(real): http://spades.bioinf.spbau.ru/spades_test_datasets/ecoli_sc/ Ecoli(reference): Escherichia coli str. K-12 substr. MG1655: http://www.ncbi.nlm.nih.gov/nuccore/49175990?report=fasta Simulated Ecoli: Used WGSIM and used the following command to generate the reads: ./wgsim -e .01 -1 75 -2 75 -d 250 -N 11909298 reference_ecoli.fa read1.fq read2.fq Staphylococcus aureus(real): http://spades.bioinf.spbau.ru/spades_test_datasets/saureus/ Staphylococcus aureus(reference): http://www.ncbi.nlm.nih.gov/nuccore/?term=Staphylococcus+aureus+subsp.+aureus+USA300_FPR3757 SAR324(real): http://spades.bioinf.spbau.ru/spades_test_datasets/SAR324/reads/ Rhodobacter sphaeroides(real): http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/ Rhodobacter sphaeroides(reference): http://gage.cbcb.umd.edu/data/Rhodobacter_sphaeroides/
CAMI
https://s3-eu-west-1.amazonaws.com/cami-data-eu/CAMI_low/RL_S001__insert_270.fq.gz
All .fastq files were converted using the following:
./idba/bin/fq2fa —-merge read1.fastq read2.fastq output.fa