LICENSE
MANIFEST
META.yml
Makefile.PL
README
README.md
bin/abacas.pl
bin/descaffold_assembly
bin/fill_gaps_with_gapfiller
bin/improve_assembly
bin/order_contigs_with_abacas
bin/read_correction_with_sga
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/Assemble/SGA/IndexAndCorrectReads.pm
lib/Bio/AssemblyImprovement/Assemble/SGA/Main.pm
lib/Bio/AssemblyImprovement/Assemble/SGA/PreprocessReads.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/PrepareForSubmission/RenameContigs.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/FastqCleanupRole.pm
lib/Bio/AssemblyImprovement/Util/UnzipFileIfNeededRole.pm
lib/Bio/AssemblyImprovement/Util/ZipFileRole.pm
lib/Bio/AssemblyImprovement/Validate/Executable.pm
t/Abacas/Iterative.t
t/Abacas/Main.t
t/Assemble/SGA/IndexAndCorrectReads.t
t/Assemble/SGA/Main.t
t/Assemble/SGA/PreprocessReads.t
t/FillGaps/GapFillerConfig.t
t/FillGaps/Iterative.t
t/Overall/CheckAllModulesCompile.t
t/PrepareForSubmission/RenameContigs.t
t/Scaffold/Descaffold.t
t/Scaffold/Iterative.t
t/Scaffold/PreprocessInputFiles.t
t/Scaffold/SSpaceConfig.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_needing_to_be_renamed.fa
t/data/contigs_with_Ns.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/reference_over_multiple_lines.fa
t/data/reverse.fastq
t/data/reverse.fastq.gz
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/dummy_abacas_script.pl
t/dummy_gap_filler_script.pl
t/dummy_sga_script
t/dummy_sga_script.pl
t/dummy_sspace_script.pl
