SSPACE-LONGREAD

Descriptions

SSPACE-longread

Requirements

• Perl
  • File::Path
  • FindBin
  • Getopt::Std
  • Text::Wrap

How to use

#format the contigs;
perl format_scaffolds.pl <CONTIG-sequences> > <CONTIG-sequences>_format.fa
#run blasr alsvolgt;
#blasr ../pacbio_reads.fasta <format-contigs> -minMatch 10 -minPctIdentity 70 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -nproc 8 -out <BLASR-output>
# perl pacbio_scaffolder.pl <BLASR-output> <CONTIG-sequences>_format.fa

Citation

Marten Boetzer and Walter Pirovano. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 2014, 15:211. doi:[10.1186/1471-2105-15-211](https://doi.org/10.1186/1471-2105-15-211)

Maintainer

卢福浩(Fu-Hao Lu)

Professor, PhD

作物逆境适应与改良国家重点实验室，生命科学学院

State Key Labortory of Crop Stress Adaptation and Improvement

College of Life Science

河南大学金明校区

Jinming Campus, Henan University

开封 475004， 中国

Kaifeng 475004, P.R.China

E-mail: LUFUHAO@HENU.EDU.CN