.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_cp_num.py
MarkerMAG/get_16s_depth.py
MarkerMAG/get_mag_depth.py
MarkerMAG/link_16s.py
MarkerMAG/matam_16s.py
MarkerMAG/polish_16s.py
MarkerMAG/preprocess_16s.py
MarkerMAG/recovery_16s.py
MarkerMAG/rename_reads.py
MarkerMAG/subsample_reads.py
MarkerMAG/uclust_16s.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
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_R1.fa
doc/vis_folder/SS_m1___SS___NODE_11_R2.fa
doc/vis_folder/SS_m1___SS___NODE_11_cbd.fa
doc/vis_folder/SS_m1___SS___NODE_11_cbd.log
doc/vis_folder/SS_m1___SS___NODE_11_cbd.sam
doc/vis_folder/SS_m1___SS___NODE_11_cbd.tablet
script_backup/tunning_rd1.py
script_backup/tunning_rd2.py
script_backup/assess_linkages/assess_linkages_GI.py
script_backup/assess_linkages/assess_linkages_OF_138.py
script_backup/assess_linkages/assess_linkages_Oral.py
script_backup/assess_linkages/assess_linkages_Pig.py
script_backup/assess_linkages/assess_linkages_Sponge.py
script_backup/assess_linkages/assess_linkages_kelp_138.py
script_backup/assess_linkages/get_depth.py
script_backup/assess_linkages/good_MAG_with_16S.py
script_backup/assess_linkages/increased_MAG_with_16s.py
script_backup/assess_linkages/s16.py