Minor

genomewalker · Nov 18, 2022 · 4f6593c · 4f6593c
1 parent 323da9c
commit 4f6593c
Showing 1 changed file with 32 additions and 24 deletions.
diff --git a/README.md b/README.md
@@ -76,32 +76,8 @@ optional arguments:
   -h, --help            show this help message and exit
   -t THREADS, --threads THREADS
                         Number of threads to use (default: 1)
-  --reference-trim-length TRIM_ENDS
-                        Exclude n bases at the ends of the reference sequences (default: 0)
-  --trim-min TRIM_MIN   Remove coverage that are below this percentile. Used for the Truncated Average
-                        Depth (TAD) calculation (default: 10)
-  --trim-max TRIM_MAX   Remove coverage that are above this percentile. Used for the Truncated Average
-                        Depth (TAD) calculation (default: 90)
   -p PREFIX, --prefix PREFIX
                         Prefix used for the output files (default: None)
-  -A MIN_READ_ANI, --min-read-ani MIN_READ_ANI
-                        Minimum read ANI to keep a read (default: 90.0)
-  -l MIN_READ_LENGTH, --min-read-length MIN_READ_LENGTH
-                        Minimum read length (default: 30)
-  -n MIN_READ_COUNT, --min-read-count MIN_READ_COUNT
-                        Minimum read count (default: 10)
-  -b MIN_EXPECTED_BREADTH_RATIO, --min-expected-breadth-ratio MIN_EXPECTED_BREADTH_RATIO
-                        Minimum expected breadth ratio (default: 0.5)
-  -e MIN_NORM_ENTROPY, --min-normalized-entropy MIN_NORM_ENTROPY
-                        Minimum normalized entropy (default: auto)
-  -g MIN_NORM_GINI, --min-normalized-gini MIN_NORM_GINI
-                        Minimum normalized Gini coefficient (default: None)
-  -B MIN_BREADTH, --min-breadth MIN_BREADTH
-                        Minimum breadth (default: 0)
-  -a MIN_AVG_READ_ANI, --min-avg-read-ani MIN_AVG_READ_ANI
-                        Minimum average read ANI (default: 90.0)
-  -c MIN_COVERAGE_EVENNESS, --min-coverage-evenness MIN_COVERAGE_EVENNESS
-                        Minimum coverage evenness (default: 0)
   -m SORT_MEMORY, --sort-memory SORT_MEMORY
                         Set maximum memory per thread for sorting; suffix K/M/G recognized (default:
                         1G)
@@ -122,6 +98,34 @@ optional arguments:
                         Chunk size for parallel processing (default: None)
   --debug               Print debug messages (default: False)
   --version             Print program version
+
+filtering arguments:
+  -A MIN_READ_ANI, --min-read-ani MIN_READ_ANI
+                        Minimum read ANI to keep a read (default: 90.0)
+  -l MIN_READ_LENGTH, --min-read-length MIN_READ_LENGTH
+                        Minimum read length (default: 30)
+  -n MIN_READ_COUNT, --min-read-count MIN_READ_COUNT
+                        Minimum read count (default: 10)
+  -b MIN_EXPECTED_BREADTH_RATIO, --min-expected-breadth-ratio MIN_EXPECTED_BREADTH_RATIO
+                        Minimum expected breadth ratio (default: 0.5)
+  -e MIN_NORM_ENTROPY, --min-normalized-entropy MIN_NORM_ENTROPY
+                        Minimum normalized entropy (default: auto)
+  -g MIN_NORM_GINI, --min-normalized-gini MIN_NORM_GINI
+                        Minimum normalized Gini coefficient (default: None)
+  -B MIN_BREADTH, --min-breadth MIN_BREADTH
+                        Minimum breadth (default: 0)
+  -a MIN_AVG_READ_ANI, --min-avg-read-ani MIN_AVG_READ_ANI
+                        Minimum average read ANI (default: 90.0)
+  -c MIN_COVERAGE_EVENNESS, --min-coverage-evenness MIN_COVERAGE_EVENNESS
+                        Minimum coverage evenness (default: 0)
+
+miscellaneous arguments:
+  --reference-trim-length TRIM_ENDS
+                        Exclude n bases at the ends of the reference sequences (default: 0)
+  --trim-min TRIM_MIN   Remove coverage that are below this percentile. Used for the Truncated Average
+                        Depth (TAD) calculation (default: 10)
+  --trim-max TRIM_MAX   Remove coverage that are above this percentile. Used for the Truncated Average
+                        Depth (TAD) calculation (default: 90)
 ```
 
 One would run filterBAM as:
@@ -169,6 +173,8 @@ The program will produce two main outputs:
     - **max_covered_bases**: Maximum number of bases covered in the reference
     - **mean_covered_bases**: Average number of bases covered in the reference
     - **coverage_mean**: Mean depth of the reference
+    - **coverage_mean_trunc**: Mean depth of the reference after removing the 10% and 90% of the coverage values (TAD80, default)
+    - **coverage_mean_trunc_len**: Length of the reference after being truncated by the TAD(X) values
     - **coverage_covered_mean**: Mean depth of the reference only counting covered bases
     - **reference_length**: Real reference length
     - **bam_reference_length**: Length reported by the BAM file
@@ -186,6 +192,8 @@ The program will produce two main outputs:
     - **cov_evenness**: Eveness of coverage as calculated [here](https://www.nature.com/articles/jhg201621).
     - **tax_abund_read**: Counts estimated using the number of reads and normalized by the reference length.
     - **tax_abund_aln**: Counts estimated using the number of alignments and normalized by the reference length.
+    - **tax_abund_tad**: Counts estimated using the estimated number of reads in the TAD region and normalized by the length of the TAD region
+    - **n_reads_tad**: Number of reads estimated in the TAD region using the formula *C = LN / G*, where C stands for the TAD coverage, N for the length of the TAD region and L for the average read length mapped to the reference.
 
 ## Applications and recommendations