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Step by step walkthrough #314

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70 changes: 36 additions & 34 deletions docs/source/step-by-step-tutorial.rst
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Expand Up @@ -637,51 +637,53 @@ Use the following command to perform binning:
--coverages $HOME/tutorial/78mbp_metagenome.coverages.tsv \
--gc-content $HOME/tutorial/78mbp_metagenome.gc_content.tsv \
--markers $HOME/tutorial/78mbp_metagenome.markers.tsv \
--output-binning $HOME/tutorial/78mbp_metagenome.binning.tsv \
--output-main $HOME/tutorial/78mbp_metagenome.main.tsv \
--clustering-method dbscan \
--completeness 20 \
--purity 90 \
--cov-stddev-limit 25 \
--gc-stddev-limit 5 \
--taxonomy $HOME/tutorial/78mbp_metagenome.taxonomy.tsv \
--output-binning $HOME/tutorial/78mbp_metagenome.binning.tsv \
--output-main $HOME/tutorial/78mbp_metagenome.main.tsv \
--starting-rank superkingdom \
--rank-filter superkingdom
--rank-filter superkingdom \
--rank-name-filter bacteria

Let us dissect the above command:

+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| Flag | Function | Requirement |
+=========================+=========================================================================================+=============+
| ``--kmers`` | Path to embedded k-mer frequencies table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--coverages`` | Path to metagenome coverages table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--gc-content`` | Path to metagenome GC contents table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--markers`` | Path to Autometa annotated markers table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--output-binning`` | Path to write Autometa binning results | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--output-main`` | Path to write Autometa main table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--clustering-method`` | Clustering algorithm to use for recursive binning. Choices dbscan (default) and hdbscan | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--completeness`` | completeness cutoff to retain cluster (default 20) | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--purity`` | purity cutoff to retain cluster (default 95) | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--cov-stddev-limit`` | coverage standard deviation limit to retain cluster (default 25) | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--gc-stddev-limit`` | GC content standard deviation limit to retain cluster (default 5) | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--taxonomy`` | Path to Autometa assigned taxonomies table | Required |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--starting-rank`` | Canonical rank at which to begin subsetting taxonomy (default: superkingdom) | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
| ``--domain`` | Kingdom to consider. Choices bacteria (default) and archaea | Optional |
+-------------------------+-----------------------------------------------------------------------------------------+-------------+
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| Flag | Function | Requirement |
+=========================+====================================================================================================================+=============+
| ``--kmers`` | Path to embedded k-mer frequencies table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--coverages`` | Path to metagenome coverages table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--gc-content`` | Path to metagenome GC contents table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--markers`` | Path to Autometa annotated markers table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--output-binning`` | Path to write Autometa binning results | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--output-main`` | Path to write Autometa main table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--clustering-method`` | Clustering algorithm to use for recursive binning. Choices dbscan (default) and hdbscan | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--completeness`` | completeness cutoff to retain cluster (default 20) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--purity`` | purity cutoff to retain cluster (default 95) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--cov-stddev-limit`` | coverage standard deviation limit to retain cluster (default 25) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--gc-stddev-limit`` | GC content standard deviation limit to retain cluster (default 5) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--taxonomy`` | Path to Autometa assigned taxonomies table | Required |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--starting-rank`` | Canonical rank at which to begin subsetting taxonomy (default: superkingdom) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--rank-filter`` | Canonical rank to subset by the value provided by ``--rank-name-filter`` default: superkingdom | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+
| ``--rank-name-filter`` | Only retrieve contigs with this value in the canonical rank column provided in ``rank-filter`` (default: bacteria) | Optional |
+-------------------------+--------------------------------------------------------------------------------------------------------------------+-------------+

You can view the complete command-line options using ``autometa-binning -h``

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