Bio_AssemblyImprovement 1.160490
- Released by
- AJPAGE
- Version
- Release Date
- 2016-02-18
- Kwalitee
- 146.88
- Core Kwalitee
- 93.75
- LINKS
Bio_AssemblyImprovement 1.160490 Latest
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- meta_yml_has_provides
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Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::AssemblyImprovement | Improve an assembly by scaffolding, contig ordering and gap closing. | metacpan | |
| Bio::AssemblyImprovement::Abacas::DelimiterRole | Moose Role for putting in delimiters for Abacas to join up contigs | metacpan | |
| Bio::AssemblyImprovement::Abacas::Iterative | Iteratively run abacas to order contigs | metacpan | |
| Bio::AssemblyImprovement::Abacas::Main | Wrapper script for Abacas, just runs it in a separate directory. | metacpan | |
| Bio::AssemblyImprovement::AdapterRemoval::Trimmomatic::Main | Remove adapter sequences from paired reads using Trimmomatic | metacpan | |
| Bio::AssemblyImprovement::Assemble::SGA::IndexAndCorrectReads | Performs SGA error correction on the reads | metacpan | |
| Bio::AssemblyImprovement::Assemble::SGA::Main | Run SGA preprocess and error correction steps | metacpan | |
| Bio::AssemblyImprovement::Assemble::SGA::PreprocessReads | Preprocess reads before error correction | metacpan | |
| Bio::AssemblyImprovement::Circlator::Main | Wrapper around circlator | metacpan | |
| Bio::AssemblyImprovement::DigitalNormalisation::Khmer::Main | Perform digital normalisation on sequencing reads | metacpan | |
| Bio::AssemblyImprovement::FillGaps::GapFiller::Config | Create the config file thats used to drive GapFiller | metacpan | |
| Bio::AssemblyImprovement::FillGaps::GapFiller::Iterative | Iteratively close gaps | metacpan | |
| Bio::AssemblyImprovement::FillGaps::GapFiller::Main | Run a single iteration of gapfiller | metacpan | |
| Bio::AssemblyImprovement::IvaQC::Main | Wrapper around iva_qc | metacpan | |
| Bio::AssemblyImprovement::PrepareForSubmission::RenameContigs | Update the names of the contigs so that the assembly can be submitted to a database like EMBL | metacpan | |
| Bio::AssemblyImprovement::PrimerRemoval::Main | Remove a set of specified primers from the edges of a read using QUASR | metacpan | |
| Bio::AssemblyImprovement::Quiver::Main | Wrapper around the quiver call | metacpan | |
| Bio::AssemblyImprovement::Scaffold::Descaffold | Given a fasta file as input, output a descaffolded multi-fasta file. | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::Config | Create the config file thats used to drive SSpace | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::Iterative | Iteratively run SSpace. | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::Main | Run one iteration of SSpace | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::OutputFilenameRole | Role for handling output filenames | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::PreprocessInputFiles | Make sure the input files are in the correct format, and paths are resolved. | metacpan | |
| Bio::AssemblyImprovement::Scaffold::SSpace::TempDirectoryRole | Role for handling temp directories | metacpan | |
| Bio::AssemblyImprovement::Util::FastaTools | Utilities for sequences in a FASTA file | metacpan | |
| Bio::AssemblyImprovement::Util::FastqTools | Take a fastq file and calculate some useful statistics and values | metacpan | |
| Bio::AssemblyImprovement::Util::GetReadLengthsRole | Role for getting the read lengths from a fastq file (useful when reads are of varying lengths) | metacpan | |
| Bio::AssemblyImprovement::Util::OrderContigsByLength | Sorts a fasta file by sequence length | metacpan | |
| Bio::AssemblyImprovement::Util::UnzipFileIfNeededRole | Role for unzipping files if needed | metacpan | |
| Bio::AssemblyImprovement::Util::ZipFileRole | Zip file | metacpan | |
| Bio::AssemblyImprovement::Validate::Executable | Validates the executable is available in the path before running it. | metacpan |