├── LICENSE ├── MANIFEST.in ├── README.md ├── _config.yml ├── _data └── navigation.yml ├── bin └── aTRAM-master │ ├── .gitignore │ ├── .travis.yml │ ├── LICENSE.txt │ ├── README.md │ ├── atram.py │ ├── atram_framer.py │ ├── atram_preprocessor.py │ ├── atram_stitcher.py │ ├── doc │ ├── atram_preprocessor_reference.md │ ├── atram_preprocessor_tutorial.md │ ├── atram_reference.md │ ├── atram_stitcher_reference.md │ ├── atram_stitcher_tutorial.md │ ├── atram_tutorial.md │ ├── images │ │ ├── atram_preprocessor.odg │ │ ├── atram_preprocessor.png │ │ ├── atram_step_1.odg │ │ ├── atram_step_1.png │ │ ├── atram_step_2.odg │ │ ├── atram_step_2.png │ │ ├── atram_step_3.odg │ │ ├── atram_step_3.png │ │ ├── atram_step_4.odg │ │ ├── atram_step_4.png │ │ ├── atram_stitcher.odg │ │ └── atram_stitcher.png │ ├── introduction.md │ ├── tips.md │ └── troubleshooting.md │ ├── environment.yml │ ├── lib │ ├── __init__.py │ ├── assembler.py │ ├── assemblers │ │ ├── __init__.py │ │ ├── abyss.py │ │ ├── base.py │ │ ├── none.py │ │ ├── spades.py │ │ ├── trinity.py │ │ └── velvet.py │ ├── bio.py │ ├── blast.py │ ├── core_atram.py │ ├── core_framer.py │ ├── core_preprocessor.py │ ├── core_stitcher.py │ ├── db.py │ ├── db_atram.py │ ├── db_preprocessor.py │ ├── db_stitcher.py │ ├── exonerate.py │ ├── log.py │ └── util.py │ ├── requirements.txt │ ├── setup.py │ ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── lib │ │ ├── __init__.py │ │ ├── assemblers │ │ │ ├── __init__.py │ │ │ └── test_base.py │ │ ├── test_bio.py │ │ ├── test_blast.py │ │ ├── test_core_atram.py │ │ ├── test_core_preprocessor.py │ │ ├── test_db.py │ │ └── test_log.py │ └── requirements-test.txt │ ├── util_atram_db_to_fasta.py │ └── util_check_requirements.py ├── docs ├── .DS_Store ├── .ipynb_checkpoints │ ├── align_contigs-checkpoint.ipynb │ ├── align_paralogs-checkpoint.ipynb │ ├── cleaning_trimming-checkpoint.ipynb │ ├── contig_assembly-checkpoint.ipynb │ ├── extract_contigs-checkpoint.ipynb │ ├── locus_selection-checkpoint.ipynb │ ├── phasing-checkpoint.ipynb │ ├── phylogeny_msc-checkpoint.ipynb │ └── reference_assembly-checkpoint.ipynb ├── _config.yml ├── _data │ └── navigation.yml ├── documentation │ ├── .DS_Store │ ├── main_doc.html │ ├── subdocs │ │ ├── align_contigs.html │ │ ├── align_paralogs.html │ │ ├── cleaning_trimming.html │ │ ├── contig_assembly.html │ │ ├── extract_contigs.html │ │ ├── locus_selection.html │ │ ├── phasing.html │ │ ├── phylogeny_msc.html │ │ └── reference_assembly.html │ └── tutorial.html ├── index.md ├── markdown │ ├── main_doc.html │ ├── main_doc.ipynb │ ├── main_doc.md │ ├── tutorial.html │ ├── tutorial.md │ └── tutorial.pdf └── notebook │ ├── .ipynb_checkpoints │ └── main_doc-checkpoint.ipynb │ ├── main_doc.ipynb │ └── subdocs │ ├── align_contigs.ipynb │ ├── align_paralogs.ipynb │ ├── cleaning_trimming.ipynb │ ├── contig_assembly.ipynb │ ├── extract_contigs.ipynb │ ├── locus_selection.ipynb │ ├── phasing.ipynb │ ├── phylogeny_msc.ipynb │ └── reference_assembly.ipynb ├── images ├── .DS_Store ├── exon_vs_contig_based_assembly.pdf ├── exon_vs_contig_based_assembly.png ├── paralog_contig_alignment.png ├── reads_to_contig.jpg ├── secapr_logo.png ├── secapr_logo_small.png ├── secapr_workflow.png ├── stacey_phylogeny.jpg ├── stacey_phylogeny.pdf └── wrong_contig.JPG ├── recipe ├── install_secapr_env.sh ├── meta.yaml ├── secapr.yml └── secapr │ ├── channeldata.json │ ├── index.html │ ├── meta.yaml │ └── noarch │ ├── current_repodata.json │ ├── current_repodata.json.bz2 │ ├── index.html │ ├── repodata.json │ ├── repodata.json.bz2 │ ├── repodata_from_packages.json │ └── repodata_from_packages.json.bz2 ├── secapr ├── .DS_Store ├── __init__.py ├── __main__.py ├── _version.py ├── add_missing_sequences.py ├── align_sequences.py ├── assemble_reads.py ├── automate_all.py ├── clean_reads.py ├── clean_reads_old.py ├── concatenate_alignments.py ├── create_consensus_from_alleles.py ├── extract_alignments_from_phyluce_get_inf_sites_output.py ├── find_target_contigs.py ├── helpers.py ├── join_exons.py ├── locus_selection.py ├── merge_probes.py ├── mpileup_fasta.py ├── paralogs_to_ref.py ├── phase_alleles.py ├── phase_alleles_provide_reference_fasta.py ├── plot_sequence_yield.py ├── process_pileup.py ├── quality_check.py ├── reference_assembly.py ├── remove_uninformative_seqs.py ├── utils.py └── varscan_vcf_2_fasta.py ├── setup.cfg ├── setup.py ├── src ├── align_paralogs.py ├── apply_read_thres_select_best_loci.py ├── check_avg_contig_length.py ├── check_target_contig_matches.py ├── estimate_pop_parameters.py ├── extract_longest_contig.py ├── fastqc_visualization.r ├── find_good_loci_for_each_sample_from_readcov_info.py ├── get_stats_from_log_files.py ├── heatmap_plot.py ├── merge_baits_for_each_locus.py ├── plot_contig_data_function.py ├── plot_contig_length_overview.py ├── plot_exon_alignment_yield.py ├── plot_exon_contig_yield.py ├── plot_exon_read_coverage.py ├── plot_exon_yield_all_datatypes.py ├── 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