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# Download sample PacBio from the PBcR websitewget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz| tar zxf -awk'NR%4==1||NR%4==2' selfSampleData/pacbio_filtered.fastq| sed's/^@/>/g'> reads.fa# Install SMARTdenovogit clone https://github.com/ruanjue/smartdenovo.git&& (cd smartdenovo; make)# Assemble (raw unitigs in wtasm.lay.utg; consensus unitigs: wtasm.cns)smartdenovo/smartdenovo.pl -c 1 reads.fa> wtasm.makmake -f wtasm.mak

SMARTdenovo is ade novo assembler for PacBio and Oxford Nanopore (ONT)data. It produces an assembly from all-vs-all raw read alignments withoutan error correction stage. It also provides tools to generate accurateconsensus sequences, though a platform dependent consensus polish tools (e.g.Quiver for PacBio or Nanopolish for ONT) are still required for higheraccuracy.

SMARTdenovo consists of several separate command line tools:wtzmo for readoverlapping,wtgbo to rescue missing overlaps,wtclp for identifyinglow-quality regions and chimaera, andwtcns orwtmsa to produce betterunitig consensus. Thesmartdenovo.pl script provides a convenient interfaceto call these programs in one go. If you do not care about the internal ofSMARTdenovo, you may simply run with:

/path/to/smartdenovo/smartdenovo.pl -p prefix -c 1 reads.fa> prefix.makmake -f prefix.mak

It calls other SMARTdenovo executables in the same directory containingsmartdenovo.pl. After assembly, the raw unitigs are reported in fileprefix.lay.utg and consensus unitigs inprefix.cns. If you want to knowmore about how SMARTdenovo works in detail, please seeREADME-tools.md.

Most time of assembly is spent on Smith-Waterm alignment, which might be not necessaryto long reads assembly. We are developping a novel algorithm, called dot matrix alignment, which is smith-waterman free.

wtzmo now supports dot matrix alignment by add option-U -1 -m 0.1.run_dmo.sh workswell on E.coli, Yeast PacBio dataset, Bacteria ERS554120, and drosopila.