The ORGanelle ASeMbler

Contents:

• Installing the ORGanelle ASeMbler
  • Availability of the ORGanelle ASeMbler
  • Prerequisites
  • Downloading and installing the ORGanelle ASeMbler
  • System level installation
  • Retrieving the sources of the ORGanelle ASeMbler
  • Compiling and installing the ORGanelle ASeMbler
• The ORGanelle ASseMbler principles
  • Sequencing strategy: Low-coverage shotgun sequencing of genomic DNA
  • The assembly graph
  • The ORGanelle ASseMbler commands
• The file formats
  • The fasta format
  • The fastq sequence format
  • The ENA flat-file format
• Assembling a mitochondrion genome with the ORGanelle ASeMbler
  • Step 1 : indexing the reads
  • Step 2 : Building the assembling graph
  • Step 3 : unfolding the graph to get the sequence
• The ORGanelle ASeMbler algorithmns
  • Seed selection
  • Graph extension
  • Graph cleanning
  • Gap filling
  • Graph unfolding

Indices and tables

• Index

• Module Index

• Search Page