.gitignore
LICENSE.txt
MANIFEST.in
README.md
setup.py
MarkerMAG/MarkerMAG_config.py
MarkerMAG/VERSION
MarkerMAG/__init__.py
MarkerMAG/barrnap_16s.py
MarkerMAG/get_16s_depth.py
MarkerMAG/get_mag_depth.py
MarkerMAG/html_parser.py
MarkerMAG/link_16s.py
MarkerMAG/link_16s_0705.py
MarkerMAG/link_16s_0716.py
MarkerMAG/link_16s_old.py
MarkerMAG/matam_16s.py
MarkerMAG/miniassembly_testing.py
MarkerMAG/polish_16s.py
MarkerMAG/preprocess_16s.py
MarkerMAG/rd2_testing.py
MarkerMAG/recovery_16s.py
MarkerMAG/rename_reads.py
MarkerMAG/stats_mini_link.py
MarkerMAG/subsample_reads.py
MarkerMAG/tmmp_6.py
MarkerMAG/tmp_1.py
MarkerMAG/tmp_2.py
MarkerMAG/tmp_3.py
MarkerMAG/tmp_4.py
MarkerMAG/tmp_5.py
MarkerMAG/tmp_6.py
MarkerMAG/tunning_rd1_mp.py
MarkerMAG/tunning_rd2_mp.py
MarkerMAG/uclust_16s.py
MarkerMAG/vis_msa.py
MarkerMAG.egg-info/PKG-INFO
MarkerMAG.egg-info/SOURCES.txt
MarkerMAG.egg-info/dependency_links.txt
MarkerMAG.egg-info/requires.txt
MarkerMAG.egg-info/top_level.txt
MarkerMAG/script_backup/link_16s copy.py
MarkerMAG/script_backup/link_16s_0510.py
MarkerMAG/script_backup/link_16s_by_assembly.py
MarkerMAG/script_backup/link_16s_drop_short_M.py
MarkerMAG/script_backup/link_16s_keep_short_M.py
MarkerMAG/script_backup/link_16s_msa.py
MarkerMAG/script_backup/rd1_testing.py
MarkerMAG/tmp/tmp_1.py
MarkerMAG/tmp/tmp_10.py
MarkerMAG/tmp/tmp_11.py
MarkerMAG/tmp/tmp_12.py
MarkerMAG/tmp/tmp_13.py
MarkerMAG/tmp/tmp_14.py
MarkerMAG/tmp/tmp_15.py
MarkerMAG/tmp/tmp_16.py
MarkerMAG/tmp/tmp_17.py
MarkerMAG/tmp/tmp_18.py
MarkerMAG/tmp/tmp_19.py
MarkerMAG/tmp/tmp_2.py
MarkerMAG/tmp/tmp_20.py
MarkerMAG/tmp/tmp_3.py
MarkerMAG/tmp/tmp_4.py
MarkerMAG/tmp/tmp_5.py
MarkerMAG/tmp/tmp_6.py
MarkerMAG/tmp/tmp_7.py
MarkerMAG/tmp/tmp_8.py
MarkerMAG/tmp/tmp_9.py
MarkerMAG/tmp/tunning_rd1.py
MarkerMAG/tmp/tunning_rd2.py
MarkerMAG/tmp/tunning_rd2_filter.py
MarkerMAG/tmp/tunning_rd2_filter_up.py
bin/MarkerMAG
doc/README_barrnap_16s.md
doc/README_matam_16s.md
doc/README_rename_reads.md
doc/README_subsample_reads.md
doc/README_uclust_16s.md
doc/example_cmds.txt
doc/images/GI_0416_identified_linkages_contig_level.txt
doc/images/Intra_genome_16S_divergence.png
doc/images/MarkerMAG_logo.jpg
doc/images/Tablet_error_report.png
doc/images/linkages_plot.png
doc/images/linking_reads.png
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_R1.fa
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_R2.fa
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_cbd.fa
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_cbd.log
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_cbd.sam
doc/vis_folder/SS_m1___SS___NODE_11_length_509157_cov_257.390468_cbd.tablet
script_backup/MarkerMAG_cmds.sh
script_backup/MarkerMAG_config.py
script_backup/MeanMAGDepth.py
script_backup/ParseMetaGTDB.py
script_backup/check_binned_16s.py
script_backup/genome_selection.py
script_backup/get_best_match_iteratively.py
script_backup/get_fake_bins.py
script_backup/get_gap_regions.py
script_backup/get_gene_location_from_gbk.py
script_backup/get_sankey_plot.R
script_backup/get_seq.py
script_backup/get_sub_count.py
script_backup/link_16s_OldCigar.py
script_backup/link_16s_by_blast.py
script_backup/link_16s_no_class_in_scripr.py
script_backup/linked_16S_scatter_plot.py
script_backup/prepare_iTOL_files_for_16S_tree.py
script_backup/rename_mag.py
script_backup/rename_matam_assemblies.py
script_backup/rm_16S.py
script_backup/subset_prokaryotes_csv.py
script_backup/subset_prokaryotes_csv_by_accession.py
script_backup/test_new_cigar_1.py
script_backup/test_new_cigar_2.py
script_backup/test_new_cigar_3.py
script_backup/tmm_24.py
script_backup/tmp-11.py
script_backup/tmp1_9.py
script_backup/tmp_1.py
script_backup/tmp_10.py
script_backup/tmp_11.py
script_backup/tmp_12.py
script_backup/tmp_13_get_table.py
script_backup/tmp_14.py
script_backup/tmp_15.py
script_backup/tmp_16.py
script_backup/tmp_17.py
script_backup/tmp_18.py
script_backup/tmp_19.py
script_backup/tmp_20.py
script_backup/tmp_21.py
script_backup/tmp_22.py
script_backup/tmp_23.py
script_backup/tmp_24_parse_sam.py
script_backup/tmp_25.py
script_backup/tmp_26.py
script_backup/tmp_27.py
script_backup/tmp_28.py
script_backup/tmp_29_get_free_living_mates_old.py
script_backup/tmp_2_depth.py
script_backup/tmp_3.py
script_backup/tmp_30_get_free_living_mates_new.py
script_backup/tmp_31.py
script_backup/tmp_32.py
script_backup/tmp_33.py
script_backup/tmp_33_sam_to_linkages_round2.py
script_backup/tmp_34.py
script_backup/tmp_35_by_blast.py
script_backup/tmp_36.py
script_backup/tmp_38_debug_Refined_28.py
script_backup/tmp_39.py
script_backup/tmp_40.py
script_backup/tmp_41.py
script_backup/tmp_42.py
script_backup/tmp_43.py
script_backup/tmp_44.py
script_backup/tmp_45.py
script_backup/tmp_5.py
script_backup/tmp_5_2.py
script_backup/tmp_6_2nd_round.py
script_backup/tmp_6_2nd_round_filter.py
script_backup/tmp_6_2nd_round_filter_old.py
script_backup/tmp_7_get_unlinks.py
script_backup/tmp_8.py
script_backup/tmp_9.py
script_backup/z_generate_abundacne.py
script_backup/z_get_16S_tree.py
script_backup/z_simulate_reads.py
script_backup/CAMI_1/parse_downloaded_files.py
script_backup/CAMI_1/tmp_1.py
script_backup/CAMI_3_hc/assess_linkages_hc.py
script_backup/CAMI_3_hc/get_bin_to_ref_hc.py
script_backup/CAMI_3_hc/map_msa_reads.py
script_backup/CAMI_3_hc/subset_hc_reads.py
script_backup/CAMI_3_hc/tmp_1.py
script_backup/CAMI_3_hc/tmp_2.py
script_backup/CAMI_3_hc/tmp_3.py
script_backup/CAMI_high/assess_linkages_high.py
script_backup/CAMI_high/s1_get_596_refs.py
script_backup/CAMI_high/s2_filter_ref_16S.py
script_backup/CAMI_high/s3_filter_reads.py
script_backup/d1_MBARC26/assess_linkages.py
script_backup/d1_MBARC26/assess_linkages_MBARC26.backup.py
script_backup/d1_MBARC26/scatter_linkages_MBARC26.py
script_backup/d1_MBARC26/tmp_1.py
script_backup/d2_GI/MAG_scfs_to_ctgs.py
script_backup/d2_GI/assess_linkages.py
script_backup/d2_GI/assess_linkages_GI.py
script_backup/d2_GI/assess_linkages_GI_138.py
script_backup/d2_GI/assess_linkages_GI_backup.py
script_backup/d2_GI/s1_get_ref_gnms.py
script_backup/d2_GI/tmp_1.py
script_backup/d2_GI/tmp_3_get_bin_depth.py
script_backup/d2_GI/000/parse_drep_Cdb_16s.py
script_backup/d2_GI/000/parse_drep_Cdb_mag.py
script_backup/d2_GI/000/rename_mag.py
script_backup/d2_GI/000/rename_matam_assemblies.py
script_backup/d3_Kelp/assess_linkages.py
script_backup/d3_Kelp/assess_linkages_128.py
script_backup/d3_Kelp/assess_linkages_kelp_138.py
script_backup/d3_Kelp/manually_check_Refined_33.py
script_backup/d3_Kelp/tmp_2.py
script_backup/d3_Kelp/tmp_3.py
script_backup/d4_Oil_Field/assess_linkages_OF_138.py
script_backup/d5_Sponge/assess_linkages_Sponge.py
script_backup/d6_Tara_SOC/get_cmd_1_wget.py
script_backup/d6_Tara_SOC/get_cmd_2_qc.py
script_backup/d6_Tara_SOC/get_cmd_3_mapping.py
script_backup/d7_Oral/assess_linkages_Oral.py