Files

• AUTHORS
• LICENSE
• MANIFEST
• META.yml
• Makefile.PL
• README
• README.md
• bin/abacas.pl
• bin/descaffold_assembly
• bin/diginorm_with_khmer
• bin/fastq_tools
• bin/fill_gaps_with_gapfiller
• bin/improve_assembly
• bin/order_contigs_with_abacas
• bin/read_correction_with_sga
• bin/remove_primers_with_quasr
• bin/rename_contigs
• bin/scaffold_with_sspace
• dist.ini
• lib/Bio/AssemblyImprovement.pm
• lib/Bio/AssemblyImprovement/Abacas/DelimiterRole.pm
• lib/Bio/AssemblyImprovement/Abacas/Iterative.pm
• lib/Bio/AssemblyImprovement/Abacas/Main.pm
• lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm
• lib/Bio/AssemblyImprovement/Assemble/SGA/IndexAndCorrectReads.pm
• lib/Bio/AssemblyImprovement/Assemble/SGA/Main.pm
• lib/Bio/AssemblyImprovement/Assemble/SGA/PreprocessReads.pm
• lib/Bio/AssemblyImprovement/Circlator/Main.pm
• lib/Bio/AssemblyImprovement/DigitalNormalisation/Khmer/Main.pm
• lib/Bio/AssemblyImprovement/FillGaps/GapFiller/Config.pm
• lib/Bio/AssemblyImprovement/FillGaps/GapFiller/Iterative.pm
• lib/Bio/AssemblyImprovement/FillGaps/GapFiller/Main.pm
• lib/Bio/AssemblyImprovement/IvaQC/Main.pm
• lib/Bio/AssemblyImprovement/PrepareForSubmission/RenameContigs.pm
• lib/Bio/AssemblyImprovement/PrimerRemoval/Main.pm
• lib/Bio/AssemblyImprovement/Quiver/Main.pm
• lib/Bio/AssemblyImprovement/Scaffold/Descaffold.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/Config.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/Iterative.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/Main.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/OutputFilenameRole.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/PreprocessInputFiles.pm
• lib/Bio/AssemblyImprovement/Scaffold/SSpace/TempDirectoryRole.pm
• lib/Bio/AssemblyImprovement/Util/FastaTools.pm
• lib/Bio/AssemblyImprovement/Util/FastqTools.pm
• lib/Bio/AssemblyImprovement/Util/GetReadLengthsRole.pm
• lib/Bio/AssemblyImprovement/Util/OrderContigsByLength.pm
• lib/Bio/AssemblyImprovement/Util/UnzipFileIfNeededRole.pm
• lib/Bio/AssemblyImprovement/Util/ZipFileRole.pm
• lib/Bio/AssemblyImprovement/Validate/Executable.pm
• software_license
• t/Abacas/Iterative.t
• t/Abacas/Main.t
• t/AdapterRemoval/Trimmomatic/Main.t
• t/Assemble/SGA/IndexAndCorrectReads.t
• t/Assemble/SGA/Main.t
• t/Assemble/SGA/PreprocessReads.t
• t/Circlator/Main.t
• t/DigitalNormalisation/Khmer/Main.t
• t/DummyQUASR.class
• t/DummyQUASR.jar
• t/DummyQUASR.java
• t/DummyQUASR.manifest.txt
• t/DummyTrimmomatic.class
• t/DummyTrimmomatic.jar
• t/DummyTrimmomatic.java
• t/DummyTrimmomatic.manifest.txt
• t/FillGaps/GapFillerConfig.t
• t/FillGaps/Iterative.t
• t/IvaQC/Main.t
• t/Overall/CheckAllModulesCompile.t
• t/PrepareForSubmission/RenameContigs.t
• t/PrimerRemoval/Main.t
• t/Quiver/Main.t
• t/Scaffold/Descaffold.t
• t/Scaffold/Iterative.t
• t/Scaffold/PreprocessInputFiles.t
• t/Scaffold/SSpaceConfig.t
• t/Util/FastaTools.t
• t/Util/FastqTools.t
• t/Util/OrderContigsByLength.t
• t/Validate/Executable.t
• t/data/contigs.fa
• t/data/contigs.scaffolded.fa
• t/data/contigs.scaffolded.fa.descaffolded
• t/data/contigs.scaffolded.fa.descaffolded.expected
• t/data/contigs_for_filtering.fa
• t/data/contigs_for_filtering.fa.filtered.min_len_1.fa
• t/data/contigs_for_filtering.fa.filtered.min_len_2.fa
• t/data/contigs_needing_sorted.fa
• t/data/contigs_needing_to_be_renamed.fa
• t/data/contigs_with_Ns.fa
• t/data/expected_circlator.log
• t/data/expected_circlator_no_merge.log
• t/data/expected_contigs_needing_sorted.fa
• t/data/expected_contigs_needing_to_be_renamed.fa
• t/data/expected_reference_over_multiple_lines.fa.union.fa
• t/data/forward.fastq
• t/data/forward.fastq.gz
• t/data/my_reference.fa
• t/data/my_reference.fa.union.fa
• t/data/primers.txt
• t/data/reference_over_multiple_lines.fa
• t/data/reverse.fastq
• t/data/reverse.fastq.gz
• t/data/shuffled.fastq
• t/data/small_contigs.fa
• t/data/small_contigs.fa.filtered
• t/data/small_contigs.fa.filtered.fa
• t/data/small_contigs.fa.gz
• t/data/split_forward.fastq
• t/data/split_reverse.fastq
• t/data/trimmo_adapters.fasta
• t/data/trimmo_reads_1.fastq
• t/data/trimmo_reads_2.fastq
• t/data/variable_length.fastq
• t/data/variable_length_zipped.fastq.gz
• t/dummy_abacas_script.pl
• t/dummy_circlator_script
• t/dummy_circlator_script_no_merge_log
• t/dummy_gap_filler_script.pl
• t/dummy_iva_qc_script
• t/dummy_iva_qc_script_raise_error.py
• t/dummy_normalise_script.py
• t/dummy_quiver_script.pl
• t/dummy_sga_script
• t/dummy_sspace_script.pl
• t/dummy_sspace_v2_script.pl
• t/requires_external.t