├── .DS_Store ├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── MarkerMAG.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── MarkerMAG ├── .DS_Store ├── MarkerMAG_config.py ├── SILVA_16S_order.fasta ├── VERSION ├── __init__.py ├── barrnap_16s.py ├── filter_sam.py ├── get_cp_num.py ├── get_mag_depth.py ├── link_16s.py ├── matam_16s.py ├── polish_16s.py ├── recovery_16s.py ├── rename_reads.py ├── subsample_reads.py ├── uclust_16s.py └── vxtractor │ ├── HMMs │ ├── SSU_archaea │ │ ├── V1leftlong.HMM │ │ ├── V1leftlong.HMM.h3f │ │ ├── V1leftlong.HMM.h3i │ │ ├── V1leftlong.HMM.h3m │ │ ├── V1leftlong.HMM.h3p │ │ ├── V1leftshort.HMM │ │ ├── V1leftshort.HMM.h3f │ │ ├── V1leftshort.HMM.h3i │ │ ├── V1leftshort.HMM.h3m │ │ ├── V1leftshort.HMM.h3p │ │ ├── V1rightlong.HMM │ │ ├── V1rightlong.HMM.h3f │ │ ├── V1rightlong.HMM.h3i │ │ ├── V1rightlong.HMM.h3m │ │ ├── V1rightlong.HMM.h3p │ │ ├── V1rightshort.HMM │ │ ├── V1rightshort.HMM.h3f │ │ ├── V1rightshort.HMM.h3i │ │ ├── V1rightshort.HMM.h3m │ │ ├── V1rightshort.HMM.h3p │ │ ├── V2leftlong.HMM │ │ ├── V2leftlong.HMM.h3f │ │ ├── V2leftlong.HMM.h3i │ │ ├── V2leftlong.HMM.h3m │ │ ├── V2leftlong.HMM.h3p │ │ ├── V2leftshort.HMM │ │ ├── V2leftshort.HMM.h3f │ │ ├── V2leftshort.HMM.h3i │ │ ├── V2leftshort.HMM.h3m │ │ ├── V2leftshort.HMM.h3p │ │ ├── V2rightlong.HMM │ │ ├── V2rightlong.HMM.h3f │ │ ├── V2rightlong.HMM.h3i │ │ ├── V2rightlong.HMM.h3m │ │ ├── V2rightlong.HMM.h3p │ │ ├── V2rightshort.HMM │ │ ├── V2rightshort.HMM.h3f │ │ ├── V2rightshort.HMM.h3i │ │ ├── V2rightshort.HMM.h3m │ │ ├── V2rightshort.HMM.h3p │ │ ├── V3leftlong.HMM │ │ ├── V3leftlong.HMM.h3f │ │ ├── V3leftlong.HMM.h3i │ │ ├── V3leftlong.HMM.h3m │ │ ├── V3leftlong.HMM.h3p │ │ ├── V3leftshort.HMM │ │ ├── V3leftshort.HMM.h3f │ │ ├── V3leftshort.HMM.h3i │ │ ├── V3leftshort.HMM.h3m │ │ ├── V3leftshort.HMM.h3p │ │ ├── V3rightlong.HMM │ │ ├── V3rightlong.HMM.h3f │ │ ├── V3rightlong.HMM.h3i │ │ ├── V3rightlong.HMM.h3m │ │ ├── V3rightlong.HMM.h3p │ │ ├── V3rightshort.HMM │ │ ├── V3rightshort.HMM.h3f │ │ ├── V3rightshort.HMM.h3i │ │ ├── V3rightshort.HMM.h3m │ │ ├── V3rightshort.HMM.h3p │ │ ├── V4leftlong.HMM │ │ ├── V4leftlong.HMM.h3f │ │ ├── V4leftlong.HMM.h3i │ │ ├── V4leftlong.HMM.h3m │ │ ├── V4leftlong.HMM.h3p │ │ ├── V4leftshort.HMM │ │ ├── V4leftshort.HMM.h3f │ │ ├── V4leftshort.HMM.h3i │ │ ├── V4leftshort.HMM.h3m │ │ ├── V4leftshort.HMM.h3p │ │ ├── V4rightlong.HMM │ │ ├── V4rightlong.HMM.h3f │ │ ├── V4rightlong.HMM.h3i │ │ ├── V4rightlong.HMM.h3m │ │ ├── V4rightlong.HMM.h3p │ │ ├── V4rightshort.HMM │ │ ├── V4rightshort.HMM.h3f │ │ ├── V4rightshort.HMM.h3i │ │ ├── V4rightshort.HMM.h3m │ │ ├── V4rightshort.HMM.h3p │ │ ├── V5leftlong.HMM │ │ ├── V5leftlong.HMM.h3f │ │ ├── V5leftlong.HMM.h3i │ │ ├── V5leftlong.HMM.h3m │ │ ├── V5leftlong.HMM.h3p │ │ ├── V5leftshort.HMM │ │ ├── V5leftshort.HMM.h3f │ │ ├── V5leftshort.HMM.h3i │ │ ├── V5leftshort.HMM.h3m │ │ ├── V5leftshort.HMM.h3p │ │ ├── V5rightlong.HMM │ │ ├── V5rightlong.HMM.h3f │ │ ├── V5rightlong.HMM.h3i │ │ ├── V5rightlong.HMM.h3m │ │ ├── V5rightlong.HMM.h3p │ │ ├── V5rightshort.HMM │ │ ├── V5rightshort.HMM.h3f │ │ ├── V5rightshort.HMM.h3i │ │ ├── V5rightshort.HMM.h3m │ │ ├── V5rightshort.HMM.h3p │ │ ├── V6leftlong.HMM │ │ ├── V6leftlong.HMM.h3f │ │ ├── V6leftlong.HMM.h3i │ │ ├── V6leftlong.HMM.h3m │ │ ├── V6leftlong.HMM.h3p │ │ ├── V6leftshort.HMM │ │ ├── V6leftshort.HMM.h3f │ │ ├── V6leftshort.HMM.h3i │ │ ├── V6leftshort.HMM.h3m │ │ ├── V6leftshort.HMM.h3p │ │ ├── V6rightlong.HMM │ │ ├── V6rightlong.HMM.h3f │ │ ├── V6rightlong.HMM.h3i │ │ ├── V6rightlong.HMM.h3m │ │ ├── V6rightlong.HMM.h3p │ │ ├── V6rightshort.HMM │ │ ├── V6rightshort.HMM.h3f │ │ ├── V6rightshort.HMM.h3i │ │ ├── V6rightshort.HMM.h3m │ │ ├── V6rightshort.HMM.h3p │ │ ├── V7leftlong.HMM │ │ ├── V7leftlong.HMM.h3f │ │ ├── V7leftlong.HMM.h3i │ │ ├── V7leftlong.HMM.h3m │ │ ├── V7leftlong.HMM.h3p │ │ ├── V7leftshort.HMM │ │ ├── V7leftshort.HMM.h3f │ │ ├── V7leftshort.HMM.h3i │ │ ├── V7leftshort.HMM.h3m │ │ ├── V7leftshort.HMM.h3p │ │ ├── V7rightlong.HMM │ │ ├── V7rightlong.HMM.h3f │ │ ├── V7rightlong.HMM.h3i │ │ ├── V7rightlong.HMM.h3m │ │ ├── V7rightlong.HMM.h3p │ │ ├── V7rightshort.HMM │ │ ├── V7rightshort.HMM.h3f │ │ ├── V7rightshort.HMM.h3i │ │ ├── V7rightshort.HMM.h3m │ │ ├── V7rightshort.HMM.h3p │ │ ├── V8leftlong.HMM │ │ ├── V8leftlong.HMM.h3f │ │ ├── V8leftlong.HMM.h3i │ │ ├── V8leftlong.HMM.h3m │ │ ├── V8leftlong.HMM.h3p │ │ ├── V8leftshort.HMM │ │ ├── V8leftshort.HMM.h3f │ │ ├── V8leftshort.HMM.h3i │ │ ├── V8leftshort.HMM.h3m │ │ ├── V8leftshort.HMM.h3p │ │ ├── V8rightlong.HMM │ │ ├── V8rightlong.HMM.h3f │ │ ├── V8rightlong.HMM.h3i │ │ ├── V8rightlong.HMM.h3m │ │ ├── V8rightlong.HMM.h3p │ │ ├── V8rightshort.HMM │ │ ├── V8rightshort.HMM.h3f │ │ ├── V8rightshort.HMM.h3i │ │ ├── V8rightshort.HMM.h3m │ │ ├── V8rightshort.HMM.h3p │ │ ├── V9leftlong.HMM │ │ ├── V9leftlong.HMM.h3f │ │ ├── V9leftlong.HMM.h3i │ │ ├── V9leftlong.HMM.h3m │ │ ├── V9leftlong.HMM.h3p │ │ ├── V9leftshort.HMM │ │ ├── V9leftshort.HMM.h3f │ │ ├── V9leftshort.HMM.h3i │ │ ├── V9leftshort.HMM.h3m │ │ ├── V9leftshort.HMM.h3p │ │ ├── V9rightlong.HMM │ │ ├── V9rightlong.HMM.h3f │ │ ├── V9rightlong.HMM.h3i │ │ ├── V9rightlong.HMM.h3m │ │ ├── V9rightlong.HMM.h3p │ │ ├── V9rightshort.HMM │ │ ├── V9rightshort.HMM.h3f │ │ ├── V9rightshort.HMM.h3i │ │ ├── V9rightshort.HMM.h3m │ │ └── V9rightshort.HMM.h3p │ └── SSU_bacteria │ │ ├── V1leftlong.HMM │ │ ├── V1leftlong.HMM.h3f │ │ ├── V1leftlong.HMM.h3i │ │ ├── V1leftlong.HMM.h3m │ │ ├── V1leftlong.HMM.h3p │ │ ├── V1leftshort.HMM │ │ ├── V1leftshort.HMM.h3f │ │ ├── V1leftshort.HMM.h3i │ │ ├── V1leftshort.HMM.h3m │ │ ├── V1leftshort.HMM.h3p │ │ ├── V1rightlong.HMM │ │ ├── V1rightlong.HMM.h3f │ │ ├── V1rightlong.HMM.h3i │ │ ├── V1rightlong.HMM.h3m │ │ ├── V1rightlong.HMM.h3p │ │ ├── V1rightshort.HMM │ │ ├── V1rightshort.HMM.h3f │ │ ├── V1rightshort.HMM.h3i │ │ ├── V1rightshort.HMM.h3m │ │ ├── V1rightshort.HMM.h3p │ │ ├── V2leftlong.HMM │ │ ├── V2leftlong.HMM.h3f │ │ ├── V2leftlong.HMM.h3i │ │ ├── V2leftlong.HMM.h3m │ │ ├── V2leftlong.HMM.h3p │ │ ├── V2leftshort.HMM │ │ ├── V2leftshort.HMM.h3f │ │ ├── V2leftshort.HMM.h3i │ │ ├── V2leftshort.HMM.h3m │ │ ├── V2leftshort.HMM.h3p │ │ ├── V2rightlong.HMM │ │ ├── V2rightlong.HMM.h3f │ │ ├── V2rightlong.HMM.h3i │ │ ├── V2rightlong.HMM.h3m │ │ ├── V2rightlong.HMM.h3p │ │ ├── V2rightshort.HMM │ │ ├── V2rightshort.HMM.h3f │ │ ├── V2rightshort.HMM.h3i │ │ ├── V2rightshort.HMM.h3m │ │ ├── V2rightshort.HMM.h3p │ │ ├── V3leftlong.HMM │ │ ├── V3leftlong.HMM.h3f │ │ ├── V3leftlong.HMM.h3i │ │ ├── V3leftlong.HMM.h3m │ │ ├── V3leftlong.HMM.h3p │ │ ├── V3leftshort.HMM │ │ ├── V3leftshort.HMM.h3f │ │ ├── V3leftshort.HMM.h3i │ │ ├── V3leftshort.HMM.h3m │ │ ├── V3leftshort.HMM.h3p │ │ ├── V3rightlong.HMM │ │ ├── V3rightlong.HMM.h3f │ │ ├── V3rightlong.HMM.h3i │ │ ├── V3rightlong.HMM.h3m │ │ ├── V3rightlong.HMM.h3p │ │ ├── V3rightshort.HMM │ │ ├── V3rightshort.HMM.h3f │ │ ├── V3rightshort.HMM.h3i │ │ ├── V3rightshort.HMM.h3m │ │ ├── V3rightshort.HMM.h3p │ │ ├── V4leftlong.HMM │ │ ├── V4leftlong.HMM.h3f │ │ ├── V4leftlong.HMM.h3i │ │ ├── V4leftlong.HMM.h3m │ │ ├── V4leftlong.HMM.h3p │ │ ├── V4leftshort.HMM │ │ ├── V4leftshort.HMM.h3f │ │ ├── V4leftshort.HMM.h3i │ │ ├── V4leftshort.HMM.h3m │ │ ├── V4leftshort.HMM.h3p │ │ ├── V4rightlong.HMM │ │ ├── V4rightlong.HMM.h3f │ │ ├── V4rightlong.HMM.h3i │ │ ├── V4rightlong.HMM.h3m │ │ ├── V4rightlong.HMM.h3p │ │ ├── V4rightshort.HMM │ │ ├── V4rightshort.HMM.h3f │ │ ├── V4rightshort.HMM.h3i │ │ ├── V4rightshort.HMM.h3m │ │ ├── V4rightshort.HMM.h3p │ │ ├── V5leftlong.HMM │ │ ├── V5leftlong.HMM.h3f │ │ ├── V5leftlong.HMM.h3i │ │ ├── V5leftlong.HMM.h3m │ │ ├── V5leftlong.HMM.h3p │ │ ├── V5leftshort.HMM │ │ ├── V5leftshort.HMM.h3f │ │ ├── V5leftshort.HMM.h3i │ │ ├── V5leftshort.HMM.h3m │ │ ├── V5leftshort.HMM.h3p │ │ ├── V5rightlong.HMM │ │ ├── V5rightlong.HMM.h3f │ │ ├── V5rightlong.HMM.h3i │ │ ├── V5rightlong.HMM.h3m │ │ ├── V5rightlong.HMM.h3p │ │ ├── V5rightshort.HMM │ │ ├── V5rightshort.HMM.h3f │ │ ├── V5rightshort.HMM.h3i │ │ ├── V5rightshort.HMM.h3m │ │ ├── V5rightshort.HMM.h3p │ │ ├── V6leftlong.HMM │ │ ├── V6leftlong.HMM.h3f │ │ ├── V6leftlong.HMM.h3i │ │ ├── V6leftlong.HMM.h3m │ │ ├── V6leftlong.HMM.h3p │ │ ├── V6leftshort.HMM │ │ ├── V6leftshort.HMM.h3f │ │ ├── V6leftshort.HMM.h3i │ │ ├── V6leftshort.HMM.h3m │ │ ├── V6leftshort.HMM.h3p │ │ ├── V6rightlong.HMM │ │ ├── V6rightlong.HMM.h3f │ │ ├── V6rightlong.HMM.h3i │ │ ├── V6rightlong.HMM.h3m │ │ ├── V6rightlong.HMM.h3p │ │ ├── V6rightshort.HMM │ │ ├── V6rightshort.HMM.h3f │ │ ├── V6rightshort.HMM.h3i │ │ ├── V6rightshort.HMM.h3m │ │ ├── V6rightshort.HMM.h3p │ │ ├── V7leftlong.HMM │ │ ├── V7leftlong.HMM.h3f │ │ ├── V7leftlong.HMM.h3i │ │ ├── V7leftlong.HMM.h3m │ │ ├── V7leftlong.HMM.h3p │ │ ├── V7leftshort.HMM │ │ ├── V7leftshort.HMM.h3f │ │ ├── V7leftshort.HMM.h3i │ │ ├── V7leftshort.HMM.h3m │ │ ├── V7leftshort.HMM.h3p │ │ ├── V7rightlong.HMM │ │ ├── V7rightlong.HMM.h3f │ │ ├── V7rightlong.HMM.h3i │ │ ├── V7rightlong.HMM.h3m │ │ ├── V7rightlong.HMM.h3p │ │ ├── V7rightshort.HMM │ │ ├── V7rightshort.HMM.h3f │ │ ├── V7rightshort.HMM.h3i │ │ ├── V7rightshort.HMM.h3m │ │ ├── V7rightshort.HMM.h3p │ │ ├── V8leftlong.HMM │ │ ├── V8leftlong.HMM.h3f │ │ ├── V8leftlong.HMM.h3i │ │ ├── V8leftlong.HMM.h3m │ │ ├── V8leftlong.HMM.h3p │ │ ├── V8leftshort.HMM │ │ ├── V8leftshort.HMM.h3f │ │ ├── V8leftshort.HMM.h3i │ │ ├── V8leftshort.HMM.h3m │ │ ├── V8leftshort.HMM.h3p │ │ ├── V8rightlong.HMM │ │ ├── V8rightlong.HMM.h3f │ │ ├── V8rightlong.HMM.h3i │ │ ├── V8rightlong.HMM.h3m │ │ ├── V8rightlong.HMM.h3p │ │ ├── V8rightshort.HMM │ │ ├── V8rightshort.HMM.h3f │ │ ├── V8rightshort.HMM.h3i │ │ ├── V8rightshort.HMM.h3m │ │ ├── V8rightshort.HMM.h3p │ │ ├── V9leftlong.HMM │ │ ├── V9leftlong.HMM.h3f │ │ ├── V9leftlong.HMM.h3i │ │ ├── V9leftlong.HMM.h3m │ │ ├── V9leftlong.HMM.h3p │ │ ├── V9leftshort.HMM │ │ ├── V9leftshort.HMM.h3f │ │ ├── V9leftshort.HMM.h3i │ │ ├── V9leftshort.HMM.h3m │ │ ├── V9leftshort.HMM.h3p │ │ ├── V9rightlong.HMM │ │ ├── V9rightlong.HMM.h3f │ │ ├── V9rightlong.HMM.h3i │ │ ├── V9rightlong.HMM.h3m │ │ ├── V9rightlong.HMM.h3p │ │ ├── V9rightshort.HMM │ │ ├── V9rightshort.HMM.h3f │ │ ├── V9rightshort.HMM.h3i │ │ ├── V9rightshort.HMM.h3m │ │ └── V9rightshort.HMM.h3p │ ├── README.txt │ ├── gpl.txt │ ├── readmefungiLSU.txt │ └── vxtractor.pl ├── README.md ├── bin └── MarkerMAG ├── dist ├── MarkerMAG-1.1.28-py3-none-any.whl └── MarkerMAG-1.1.28.tar.gz ├── doc ├── .DS_Store ├── README_GC_bias.md ├── README_arguments.md ├── README_barrnap_16s.md ├── README_example_cmds.md ├── README_matam_16s.md ├── README_rename_reads.md ├── README_subsample_reads.md ├── README_uclust_16s.md ├── example_cmds.txt ├── images │ ├── FP_GC_bias.png │ ├── FP_read_coverage.png │ ├── GI_0416_identified_linkages_contig_level.txt │ ├── Intra_genome_16S_divergence.png │ ├── MarkerMAG_workflow.png │ ├── Tablet_error_report.png │ ├── linkages_plot_1.png │ ├── linkages_plot_2.png │ ├── linking_reads.png │ ├── logo.jpg │ └── subsample.png └── vis_folder │ ├── SS_m1___SS___NODE_11_R1.fa │ ├── SS_m1___SS___NODE_11_R2.fa │ ├── SS_m1___SS___NODE_11_cbd.fa │ ├── SS_m1___SS___NODE_11_cbd.log │ ├── SS_m1___SS___NODE_11_cbd.sam │ └── SS_m1___SS___NODE_11_cbd.tablet ├── script_backup ├── .DS_Store ├── 000 │ ├── .DS_Store │ ├── Tax4Fun2.sh │ ├── Tax4Fun2_Kelp.py │ ├── assess_cp_num_GI.py │ ├── get_16s_copy_num_1.py │ ├── get_16s_copy_num_2.py │ ├── get_16s_copy_num_3_only_uniq.py │ ├── get_16s_copy_num_4_non_overlapping.py │ ├── get_cp_num.sh │ ├── get_cp_num_b1.py │ ├── get_ref_16s_copy_num.py │ ├── get_ref_16s_copy_num_uniq.py │ ├── get_ref_genome_metadata.py │ ├── keep_both_mapped.py │ ├── opt_estimations.py │ ├── preprocess_16s.py │ ├── subsample_silva_16S.py │ ├── tmp_1.py │ ├── tmp_10_rm_overlapping_reads.py │ ├── tmp_11.py │ ├── tmp_12.py │ ├── tmp_13_similarity_distribution.py │ ├── tmp_14.py │ ├── tmp_15_reviewer_comments_1.py │ ├── tmp_15_reviewer_comments_2.py │ ├── tmp_15_reviewer_comments_3.py │ ├── tmp_16.py │ ├── tmp_2_simulate_reads.py │ ├── tmp_3.py │ ├── tmp_4.py │ ├── tmp_5.py │ ├── tmp_6_blast.py │ ├── tmp_7.py │ ├── tmp_8_sep_reads.py │ └── tmp_9.py ├── MANIFEST ├── MANIFEST.in ├── assess_linkages │ ├── assess_linkages_GI.py │ ├── assess_linkages_OF_138.py │ ├── assess_linkages_Oral.py │ ├── assess_linkages_Pig.py │ ├── assess_linkages_Sponge.py │ ├── assess_linkages_kelp_138.py │ ├── get_depth.py │ ├── good_MAG_with_16S.py │ ├── increased_MAG_with_16s.py │ └── s16.py ├── gc_bias.py ├── get_16s_depth.py ├── tunning_rd1.py ├── tunning_rd2.py └── tunning_rd2_mini_to_mag.py └── setup.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/songweizhi/MarkerMAG/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitignore: 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