Andrew Page > Bio_AssemblyImprovement

Bio_AssemblyImprovement

This Release Bio_AssemblyImprovement-1.140300  [Download] [Browse 30 Jan 2014
Other Releases
Links Discussion Forum ] [ View/Report Bugs (0) ] [ Website ] [ Dependencies ] [ Other Tools ]
Repository https://github.com/sanger-pathogens/assembly_improvement.git
CPAN Testers FAIL (316)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The GNU General Public License, Version not specified
Special Files
LICENSE
Makefile.PL
MANIFEST
META.yml
README

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::Assemble::SGA::IndexAndCorrectReads Performs SGA error correction on the reads      
Bio::AssemblyImprovement::Assemble::SGA::Main Run SGA preprocess and error correction steps      
Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads Preprocess reads before error correction      
Bio::AssemblyImprovement::DigitalNormalisation::Khmer::Main Perform digital normalisation on sequencing reads      
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::PrepareForSubmission::RenameContigs Update the names of the contigs so that the assembly can be submitted to a database like EMBL      
Bio::AssemblyImprovement::PrimerRemoval::Main Remove a set of specified primers from the edges of a read using QUASR      
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::Util::FastaTools Utilities for sequences in a FASTA file      
Bio::AssemblyImprovement::Util::FastqTools Take a fastq file and calculate some useful statistics and values      
Bio::AssemblyImprovement::Util::GetReadLengthsRole Role for getting the read lengths from a fastq file (useful when reads are of varying lengths)      
Bio::AssemblyImprovement::Util::OrderContigsByLength Sorts a fasta file by sequence length      
Bio::AssemblyImprovement::Util::UnzipFileIfNeededRole Role for unzipping files if needed      
Bio::AssemblyImprovement::Util::ZipFileRole Zip file      
Bio::AssemblyImprovement::Validate::Executable Validates the executable is available in the path before running it.      

Documentation

abacas.pl Algorithm Based Automatic Contiguation of Assembled Sequences  
descaffold_assembly Given an assembly in FASTA format, output a descaffolded assembly.  
diginorm_with_khmer Given a fastq file, it performs digital normalisation on the reads using khmer  
fastq_tools  
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  
read_correction_with_sga Given a fastq file(s), perform SGA preprocessing and error correction  
remove_primers_with_quasr Given a forward and reverse FASTQ file and a file with primers, it will remove the primers if it appears within a specified distance from the beginning of the read  
rename_contigs Given an assembly, rename the contigs iteratively  
scaffold_with_sspace Given an assembly and some reads in fastq format, try and scaffold the assembly.  

Other Files

README.md