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Merged
WardDeb merged 1 commit into from
Mar 11, 2024
Merged

version boost, and include GRCm39 in ESS docs #1297

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32 changes: 17 additions & 15 deletions docs/content/feature/effectiveGenomeSize.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@ The effective genome size for a number of genomes using this method is given bel
+---------------+------------------+
|GRCm38 | 2652783500 |
+---------------+------------------+
|GRCm39 | 2654621783 |
+---------------+------------------+
|dm3 | 162367812 |
+---------------+------------------+
|dm6 | 142573017 |
Expand All @@ -44,18 +46,18 @@ These are then based on the read length.
We can approximate these values for various read lengths using the `khmer program <https://khmer.readthedocs.io/en/latest/>`__ program and ``unique-kmers.py`` in particular.
A table of effective genome sizes given a read length using this method is provided below:

+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|Read length | GRCh37 | GRCh38 | T2T/CHM13CAT_v2 | GRCm37 | GRCm38 | dm3 | dm6 | GRCz10 | GRCz11 | WBcel235 | TAIR10 |
+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
|50 | 2685511454 | 2701495711 | 2725240337 | 2304947876 | 2308125299 | 130428510 | 125464678 | 1195445541 | 1197575653 | 95159402 | 114339094 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|75 | 2736124898 | 2747877702 | 2786136059 | 2404646149 | 2407883243 | 135004387 | 127324557 | 1251132611 | 1250812288 | 96945370 | 115317469 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|100 | 2776919708 | 2805636231 | 2814334875 | 2462480910 | 2467481008 | 139647132 | 129789773 | 1280188944 | 1280354977 | 98259898 | 118459858 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|150 | 2827436883 | 2862010428 | 2931551487 | 2489384085 | 2494787038 | 144307658 | 129940985 | 1312207019 | 1311832909 | 98721103 | 118504138 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|200 | 2855463800 | 2887553103 | 2936403235 | 2513019076 | 2520868989 | 148523810 | 132508963 | 1321355041 | 1322366338 | 98672558 | 117723393 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|250 | 2855044784 | 2898802627 | 2960856300 | 2528988583 | 2538590322 | 151901455 | 132900923 | 1339205109 | 1342093482 | 101271756 | 119585546 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|Read length | GRCh37 | GRCh38 | T2T/CHM13CAT_v2 | GRCm37 | GRCm38 | GRCm39 | dm3 | dm6 | GRCz10 | GRCz11 | WBcel235 | TAIR10 |
+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+=================+
|50 | 2685511454 | 2701495711 | 2725240337 | 2304947876 | 2308125299 | 2309746861 | 130428510 | 125464678 | 1195445541 | 1197575653 | 95159402 | 114339094 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|75 | 2736124898 | 2747877702 | 2786136059 | 2404646149 | 2407883243 | 2410055689 | 135004387 | 127324557 | 1251132611 | 1250812288 | 96945370 | 115317469 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|100 | 2776919708 | 2805636231 | 2814334875 | 2462480910 | 2467481008 | 2468088461 | 139647132 | 129789773 | 1280188944 | 1280354977 | 98259898 | 118459858 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|150 | 2827436883 | 2862010428 | 2931551487 | 2489384085 | 2494787038 | 2495461690 | 144307658 | 129940985 | 1312207019 | 1311832909 | 98721103 | 118504138 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|200 | 2855463800 | 2887553103 | 2936403235 | 2513019076 | 2520868989 | 2521902382 | 148523810 | 132508963 | 1321355041 | 1322366338 | 98672558 | 117723393 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
|250 | 2855044784 | 2898802627 | 2960856300 | 2528988583 | 2538590322 | 2538633971 | 151901455 | 132900923 | 1339205109 | 1342093482 | 101271756 | 119585546 |
+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+-----------------+
2 changes: 1 addition & 1 deletion galaxy/wrapper/deepTools_macros.xml
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@@ -1,7 +1,7 @@
<macros>

<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
<token name="@TOOL_VERSION@">3.5.5</token>
<token name="@TOOL_VERSION@">3.5.6</token>
<token name="@GALAXY_VERSION@">22.05</token>
<xml name="requirements">
<requirements>
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ requires = [

[project]
name = "deepTools"
version = "3.5.5"
version = "3.5.6"
authors = [
{name="Fidel Ramirez"},
{name="Devon P Ryan"},
Expand Down