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Bio_AssemblyImprovement-1.160490
River stage zero No dependents
++

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.

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::AdapterRemoval::Trimmomatic::Main
Remove adapter sequences from paired reads using Trimmomatic
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::Circlator::Main
Wrapper around circlator
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::IvaQC::Main
Wrapper around iva_qc
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::Quiver::Main
Wrapper around the quiver call
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.

Other files