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Bio_AssemblyImprovement-1.123530
River stage zero No dependents
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Documentation

abacas.pl
Algorithm Based Automatic Contiguation of Assembled Sequences
descaffold_assembly
Given an assembly in FASTA format, output a descaffolded assembly.
fill_gaps_with_gapfiller
Given an assembly iteratively fill gaps
improve_assembly
Given an assembly, some reads and optionally a reference, reduce the number of contigs and fill gaps.
order_contigs_with_abacas
Given an assembly and a reference, order the contigs
scaffold_with_sspace
Given an assembly and some reads in fastq format, try and scaffold the assembly.

Modules

Bio::AssemblyImprovement
Improve an assembly by scaffolding, contig ordering and gap closing.
Bio::AssemblyImprovement::Abacas::DelimiterRole
Moose Role for putting in delimiters for Abacas to join up contigs
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
Bio::AssemblyImprovement::FillGaps::GapFiller::Main
Run a single iteration of gapfiller
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
Iteratively run SSpace.
Bio::AssemblyImprovement::Scaffold::SSpace::Main
Run one iteration of SSpace
Bio::AssemblyImprovement::Scaffold::SSpace::OutputFilenameRole
Role for handling output filenames
Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles
Make sure the input files are in the correct format, and paths are resolved.
Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole
Role for handling temp directories
Bio::AssemblyImprovement::Validate::Executable
Validates the executable is available in the path before running it.

Other files