├── .gitignore ├── .travis.yml ├── AUTHORS ├── CHANGELOG.md ├── README.md ├── bin ├── abacas.pl ├── descaffold_assembly ├── diginorm_with_khmer ├── fastq_tools ├── fill_gaps_with_gapfiller ├── improve_assembly ├── order_contigs_with_abacas ├── read_correction_with_sga ├── remove_primers_with_quasr ├── rename_contigs └── scaffold_with_sspace ├── dist.ini ├── example ├── README.md ├── S.welt.10259.plasmid_1.fastq.gz ├── S.welt.10259.plasmid_2.fastq.gz └── example_output │ ├── final_improved_assembly.fa │ └── velvet_optimiser_assembly.fa ├── lib └── Bio │ ├── AssemblyImprovement.pm │ └── AssemblyImprovement │ ├── Abacas │ ├── DelimiterRole.pm │ ├── Iterative.pm │ └── Main.pm │ ├── AdapterRemoval │ └── Trimmomatic │ │ └── Main.pm │ ├── Assemble │ └── SGA │ │ ├── IndexAndCorrectReads.pm │ │ ├── Main.pm │ │ └── PreprocessReads.pm │ ├── Circlator │ └── Main.pm │ ├── DigitalNormalisation │ └── Khmer │ │ └── Main.pm │ ├── FillGaps │ └── GapFiller │ │ ├── Config.pm │ │ ├── Iterative.pm │ │ └── Main.pm │ ├── IvaQC │ └── Main.pm │ ├── PrepareForSubmission │ └── RenameContigs.pm │ ├── PrimerRemoval │ └── Main.pm │ ├── Quiver │ └── Main.pm │ ├── Scaffold │ ├── Descaffold.pm │ └── SSpace │ │ ├── Config.pm │ │ ├── Iterative.pm │ │ ├── Main.pm │ │ ├── OutputFilenameRole.pm │ │ ├── PreprocessInputFiles.pm │ │ └── TempDirectoryRole.pm │ ├── Util │ ├── FastaTools.pm │ ├── FastqTools.pm │ ├── GetReadLengthsRole.pm │ ├── OrderContigsByLength.pm │ ├── UnzipFileIfNeededRole.pm │ └── ZipFileRole.pm │ └── Validate │ └── Executable.pm ├── software-license └── t ├── Abacas ├── Iterative.t └── Main.t ├── AdapterRemoval └── Trimmomatic │ └── Main.t ├── Assemble └── SGA │ ├── IndexAndCorrectReads.t │ ├── Main.t │ └── PreprocessReads.t ├── Circlator └── Main.t ├── DigitalNormalisation └── Khmer │ └── Main.t ├── DummyQUASR.class ├── DummyQUASR.jar ├── DummyQUASR.java ├── DummyQUASR.manifest.txt ├── DummyTrimmomatic.class ├── DummyTrimmomatic.jar ├── DummyTrimmomatic.java ├── DummyTrimmomatic.manifest.txt ├── FillGaps ├── GapFillerConfig.t └── Iterative.t ├── IvaQC └── Main.t ├── Overall └── CheckAllModulesCompile.t ├── PrepareForSubmission └── RenameContigs.t ├── PrimerRemoval └── Main.t ├── Quiver └── Main.t ├── Scaffold ├── Descaffold.t ├── Iterative.t ├── PreprocessInputFiles.t └── SSpaceConfig.t ├── Util ├── FastaTools.t ├── FastqTools.t └── OrderContigsByLength.t ├── Validate └── Executable.t ├── data ├── contigs.fa ├── contigs.scaffolded.fa ├── contigs.scaffolded.fa.descaffolded ├── contigs.scaffolded.fa.descaffolded.expected ├── contigs_for_filtering.fa ├── contigs_for_filtering.fa.filtered.min_len_1.fa ├── contigs_for_filtering.fa.filtered.min_len_2.fa ├── contigs_needing_sorted.fa ├── contigs_needing_to_be_renamed.fa ├── contigs_with_Ns.fa ├── expected_circlator.log ├── expected_circlator_no_merge.log ├── expected_contigs_needing_sorted.fa ├── expected_contigs_needing_to_be_renamed.fa ├── expected_reference_over_multiple_lines.fa.union.fa ├── forward.fastq ├── forward.fastq.gz ├── my_reference.fa ├── my_reference.fa.union.fa ├── primers.txt ├── reference_over_multiple_lines.fa ├── reverse.fastq ├── reverse.fastq.gz ├── shuffled.fastq ├── small_contigs.fa ├── small_contigs.fa.filtered ├── small_contigs.fa.filtered.fa ├── small_contigs.fa.gz ├── split_forward.fastq ├── split_reverse.fastq ├── trimmo_adapters.fasta ├── trimmo_reads_1.fastq ├── trimmo_reads_2.fastq ├── variable_length.fastq └── variable_length_zipped.fastq.gz ├── dummy_abacas_script.pl ├── dummy_circlator_script ├── dummy_circlator_script_no_merge_log ├── dummy_gap_filler_script.pl ├── dummy_iva_qc_script ├── dummy_iva_qc_script_raise_error.py ├── dummy_normalise_script.py ├── dummy_quiver_script.pl ├── dummy_sga_script ├── dummy_sspace_script.pl └── dummy_sspace_v2_script.pl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/assembly_improvement/HEAD/.gitignore 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