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Bio_Assembly_Improvement-20121015.0944
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Documentation

descaffold_assembly
fill_gaps_with_gapfiller
improve_assembly
order_contigs_with_abacas
scaffold_with_sspace

Modules

Bio::AssemblyImprovement::Abacas::Iterative
Iteratively run abacas to order contigs
Bio::AssemblyImprovement::Abacas::Main
Wrapper script for Abacas, just runs it in a separate directory.
Bio::AssemblyImprovement::FillGaps::GapFiller::Config
Create the config file thats used to drive GapFiller
Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative
Iteratively close gaps. Use different mappers in rotation, picking the most confident gaps first
Bio::AssemblyImprovement::FillGaps::GapFiller::Main
Create the config file thats used to drive SSpace
Bio::AssemblyImprovement::Scaffold::Descaffold
given a fasta file as input, output a descaffolded multi-fasta file.
Bio::AssemblyImprovement::Scaffold::SSpace::Config
Create the config file thats used to drive SSpace
Bio::AssemblyImprovement::Scaffold::SSpace::Iterative
Create the config file thats used to drive SSpace
Bio::AssemblyImprovement::Scaffold::SSpace::Main
Create the config file thats used to drive SSpace
Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles
make sure the input files are in the correct format, and paths are resolved. This object needs to be kept in scope because it creates temp files which are cleaned up when it goes out of scope.

Provides

Bio::AssemblyImprovement::Abacas::DelimiterRole
in lib/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm
Bio::AssemblyImprovement::Scaffold::SSpace::OutputFilenameRole
in lib/Bio/AssemblyImprovement/Scaffold/SSpace/OutputFilenameRole.pm
Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole
in lib/Bio/AssemblyImprovement/Scaffold/SSpace/TempDirectoryRole.pm

Other files