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/usr/bin/circlator
/usr/lib/python3/dist-packages/circlator-1.5.5.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/circlator-1.5.5.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/circlator-1.5.5.egg-info/requires.txt
/usr/lib/python3/dist-packages/circlator-1.5.5.egg-info/top_level.txt
/usr/lib/python3/dist-packages/circlator/__init__.py
/usr/lib/python3/dist-packages/circlator/assemble.py
/usr/lib/python3/dist-packages/circlator/assembly.py
/usr/lib/python3/dist-packages/circlator/bamfilter.py
/usr/lib/python3/dist-packages/circlator/clean.py
/usr/lib/python3/dist-packages/circlator/common.py
/usr/lib/python3/dist-packages/circlator/data/dnaA.fasta
/usr/lib/python3/dist-packages/circlator/data/test_contigs.fa
/usr/lib/python3/dist-packages/circlator/data/test_for_reads.fa
/usr/lib/python3/dist-packages/circlator/data/test_make_data.sh
/usr/lib/python3/dist-packages/circlator/data/test_reads.fq.gz
/usr/lib/python3/dist-packages/circlator/data/test_ref.fa
/usr/lib/python3/dist-packages/circlator/data/test_ref.fa.fai
/usr/lib/python3/dist-packages/circlator/dnaa.py
/usr/lib/python3/dist-packages/circlator/external_progs.py
/usr/lib/python3/dist-packages/circlator/mapping.py
/usr/lib/python3/dist-packages/circlator/merge.py
/usr/lib/python3/dist-packages/circlator/minimus2.py
/usr/lib/python3/dist-packages/circlator/program.py
/usr/lib/python3/dist-packages/circlator/start_fixer.py
/usr/lib/python3/dist-packages/circlator/tasks/__init__.py
/usr/lib/python3/dist-packages/circlator/tasks/all.py
/usr/lib/python3/dist-packages/circlator/tasks/assemble.py
/usr/lib/python3/dist-packages/circlator/tasks/bam2reads.py
/usr/lib/python3/dist-packages/circlator/tasks/clean.py
/usr/lib/python3/dist-packages/circlator/tasks/fixstart.py
/usr/lib/python3/dist-packages/circlator/tasks/get_dnaa.py
/usr/lib/python3/dist-packages/circlator/tasks/mapreads.py
/usr/lib/python3/dist-packages/circlator/tasks/merge.py
/usr/lib/python3/dist-packages/circlator/tasks/minimus2.py
/usr/lib/python3/dist-packages/circlator/tasks/progcheck.py
/usr/lib/python3/dist-packages/circlator/tasks/test.py
/usr/lib/python3/dist-packages/circlator/tasks/version.py
/usr/lib/python3/dist-packages/circlator/tests/assemble_test.py
/usr/lib/python3/dist-packages/circlator/tests/assembly_test.py
/usr/lib/python3/dist-packages/circlator/tests/bamfilter_test.py
/usr/lib/python3/dist-packages/circlator/tests/clean_test.py
/usr/lib/python3/dist-packages/circlator/tests/common_test.py
/usr/lib/python3/dist-packages/circlator/tests/data/assemble_test.dummy_reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa
/usr/lib/python3/dist-packages/circlator/tests/data/assemble_test_rename_canu_contigs.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.assembly_graph.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_from_spades_after_3_6_1.contigs.paths
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_from_spades_before_3_6_1.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_only_contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/assembly_graph.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_post_3_6_1/contigs.paths
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_circular_contigs_spades_pre_3_6_1/contigs.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_get_contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph/contigs.paths
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/assembly_graph.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_no_contigs_paths/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/assembly_graph.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_post_3_6_1_ok/contigs.paths
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_no_fastg/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fasta
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_init_spades_pre_3_6_1_ok/contigs.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/assembly_test_spades_contigs_paths_to_dict.contigs.paths
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_all_reads_from_contig.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_all_reads_from_contig.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_break_reads.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_break_reads.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_break_reads.broken_reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_check_contigs_to_use.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_exclude_region.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_exclude_region.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_exclude_region.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_exclude_region.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_all_unmapped_reads.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_contigs_to_use.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_contigs_to_use.infile
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_ref_lengths.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_end.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_end.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_end.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_start.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_start.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_get_region_start.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run.make_reads_and_bam.sh
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run.ref.fa.fai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_discard_unmapped.out.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fa
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_no_qual.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_no_qual.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_with_qual.bam
/usr/lib/python3/dist-packages/circlator/tests/data/bamfilter_test_run_with_qual.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_clean_contigs.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_clean_contigs.out.fa
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_contigs_to_keep
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_load_nucmer_hits.coords
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_remove_small_contigs.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_remove_small_contigs.out.fa
/usr/lib/python3/dist-packages/circlator/tests/data/clean_test_write_log.log
/usr/lib/python3/dist-packages/circlator/tests/data/common_test_file_exists
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_aligned_read_to_read.bam
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_bwa_index.fa
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_bwa_mem.reads.fq
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_bwa_mem.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_contigs_dict_to_file.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_get_spades_circular_nodes.fastg
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.1.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.1.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.1.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.2.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.2.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_hits_to_new_seq.2.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_index_fasta.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_index_fasta.fa.fai
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_load_nucmer_hits.coords
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test1.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test2.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test3.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_bridged_contig_pair.test4.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_pair.test1.coords
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_pair.test2.coords
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_merge_pair.test3.coords
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_nucmer_hits_to_potential_join.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_original.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_reassembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_write_act_files.coords
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_write_act_files.expected.crunch
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_write_act_files.expected.sh
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_write_act_files.qry.fa
/usr/lib/python3/dist-packages/circlator/tests/data/merge_test_write_act_files.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test.dummy_input_assembly.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test.write_split_contig.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_initial_merge.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_initial_merge.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2_on_each_contig.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.expected.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.fa
/usr/lib/python3/dist-packages/circlator/tests/data/minimus2_test_run_minimus2_on_one_contig.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_init_contigs.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_init_dnaA.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_init_ignore_ids
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_rearrange_contigs.expect.log
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_rearrange_contigs.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_bit_of_everything.ignore
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/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_ignore_all.to_ignore
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/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa
/usr/lib/python3/dist-packages/circlator/tests/data/start_fixer_write_renamed_contigs.fa
/usr/lib/python3/dist-packages/circlator/tests/dnaa_test.py
/usr/lib/python3/dist-packages/circlator/tests/external_progs_test.py
/usr/lib/python3/dist-packages/circlator/tests/mapping_test.py
/usr/lib/python3/dist-packages/circlator/tests/merge_test.py
/usr/lib/python3/dist-packages/circlator/tests/minimus2_test.py
/usr/lib/python3/dist-packages/circlator/tests/start_fixer_test.py
/usr/lib/python3/dist-packages/circlator/versions.py
/usr/share/doc/circlator/README.md.gz
/usr/share/doc/circlator/README.test
/usr/share/doc/circlator/changelog.Debian.gz
/usr/share/doc/circlator/changelog.gz
/usr/share/doc/circlator/copyright
/usr/share/doc/circlator/examples/assemble_test.py
/usr/share/doc/circlator/examples/assembly_test.py
/usr/share/doc/circlator/examples/bamfilter_test.py
/usr/share/doc/circlator/examples/clean_test.py
/usr/share/doc/circlator/examples/common_test.py
/usr/share/doc/circlator/examples/data.tar.xz
/usr/share/doc/circlator/examples/dnaa_test.py
/usr/share/doc/circlator/examples/external_progs_test.py
/usr/share/doc/circlator/examples/mapping_test.py
/usr/share/doc/circlator/examples/merge_test.py
/usr/share/doc/circlator/examples/minimus2_test.py
/usr/share/doc/circlator/examples/start_fixer_test.py
/usr/share/doc/circlator/run-unit-test
/usr/share/man/man1/circlator.1.gz