.github/workflows/basic.yml

+name: SPAdes basic tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    
+    strategy:
+      matrix: 
+        os: [ ubuntu-latest, macos-latest ]
+    
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+    
+    - name: prepare
+      run: cd assembler && mkdir build_spades
+
+    - name: cmake
+      run: cd assembler/build_spades && cmake - G "Unix Makefiles" ../src
+
+    - name: compile include test
+      run: make -C assembler/build_spades/test/include_test include_test
+
+    - name: compile debruijn test
+      run: make -C assembler/build_spades/test/debruijn debruijn_test
+
+    - name: include check
+      run: cd assembler && build_spades/bin/include_test
+      
+    - name: debruijn check
+      run: cd assembler && build_spades/bin/debruijn_test

.github/workflows/spades-test.yml

+name: SPAdes 1k test
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    
+    strategy:
+      matrix: 
+        os: [ ubuntu-latest, macos-latest ]
+    
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+
+    - name: compile
+      run: assembler/spades_compile.sh -j3
+
+    - name: multi-cell mode check
+      run: bin/spades.py --test
+    - name: single-cell mode check
+      run: bin/spades.py --sc --test
+    - name: plasmid mode check
+      run: bin/plasmidspades.py --test
+    - name: metagenomic mode check
+      run: bin/metaspades.py --test

assembler/.clang-format

+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeCategories: 
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Auto
+TabWidth:        8
+UseTab:          Never
+...
+

assembler/LICENSE

@@ -28,8 +28,6 @@ Current SPAdes contributors:
 
     Dmitry Antipov,
     Elena Bushmanova,
-    Vasisliy Ershov,
-    Yuriy Gorshkov,
     Alexey Gurevich,
     Anton Korobeynikov,
     Olga Kunyavskaya,
@@ -46,6 +44,8 @@ Also contributed:
     Max Alekseyev,
     Anton Bankevich,
     Mikhail Dvorkin,
+    Vasisliy Ershov,
+    Yuriy Gorshkov,
     Alexander Kulikov,
     Valery Lesin,
     Sergey Nikolenko,

assembler/VERSION

-3.13.1
+3.14.0

assembler/changelog.html

@@ -3,6 +3,34 @@
 
 <h2>SPAdes Genome Assembler changelog</h2>
 
+<h3>SPAdes 3.14.0, 27 December 2019</h3>
+
+<p>NEW: BiosyntheticSPAdes pipeline for predicting Biosynthetic Gene Clusters.</p>
+
+<p>NEW: Hybrid transcriptome assembly with rnaSPAdes.</p>
+
+<p>NEW: Plasmid detection from metagenomic samples.</p>
+
+<p>NEW: Special <code>--isolate</code> option for assembly of standard datasets with good coverage (>100x).</p>
+
+<p>NEW: Standalone tool for reads filtration based on k-mer coverage.</p>
+
+<p>NEW: Standalone tool for estimating approximate number of unique k-mers in reads.</p>
+
+<p>CHANGE: Improved SPAligner tool.</p>
+
+<p>CHANGE: Reworked python code, faster sequence transfer between different k-mer stages.</p>
+
+<p>CHANGE: Multiple performance improvements in graph construction and simplification procedures.</p>
+
+<p>FIX: BWA aligner failure for large graphs.</p>
+
+<p>FIX: Failure when additional paired-end libraries with reads shorter than final k-mer length are provided.</p>
+
+<h3>SPAdes 3.13.2, 31 October 2019</h3>
+
+<p>FIX: Incorrect k-mer size estimation in rnaSPAdes.</p>
+
 <h3>SPAdes 3.13.1, 11 April 2019</h3>
 
 <p>CHANGE: Removed BayesHammer from rnaSPAdes pipeline.</p>

assembler/configs/cap/gaf.info

-cache_root ./data/cap/cache
-desc_file_name description.txt
-default_log_filename diversities_log.txt
-; w for rewrite, a for append; on first launch recreated anyway, though
-default_log_file_mode a

assembler/configs/debruijn/bgc_mode.info

+mode    bgc
+set_of_hmms none
\ No newline at end of file

assembler/configs/debruijn/config.info

@@ -11,9 +11,6 @@ K		55
 ;FIXME introduce isolate mode
 mode base
 
-;FIXME remove!
-run_mode false
-project_name    TOY_DATASET
 dataset         ./configs/debruijn/toy.info
 log_filename    log.properties
 
@@ -32,18 +29,22 @@ max_threads		8
 max_memory      120; in Gigabytes
 buffer_size     512; in Megabytes
 
-entry_point construction
+entry_point read_conversion
+;entry_point construction
 ;entry_point simplification
 ;entry_point hybrid_aligning
 ;entry_point late_pair_info_count
 ;entry_point distance_estimation
 ;entry_point repeat_resolving
 
+checkpoints none
 developer_mode true
 scaffold_correction_mode false
 
 ; enabled (1) or disabled (0) repeat resolution (former "paired_mode")
 rr_enable true
+; 0 for graph N50
+min_edge_length_for_is_count 0
 
 ;preserve raw paired index after distance estimation
 preserve_raw_paired_index false
@@ -143,7 +144,7 @@ lcer
 
 pacbio_processor
 {
-    bwa_length_cutoff 200
+    internal_length_cutoff 200
 ;align and traverse.
     compression_cutoff 0.6
     path_limit_stretching 1.3
@@ -152,6 +153,7 @@ pacbio_processor
     max_vertex_in_dijkstra 2000
 ;gap_closer
     long_seq_limit 400
+    enable_gap_closing true
     pacbio_min_gap_quantity 2
     contigs_min_gap_quantity 1
     max_contigs_gap_length 10000

assembler/configs/debruijn/isolate_mode.info

+mode isolate
+
+#include "careful_mode.info"
+

assembler/configs/debruijn/log.properties

@@ -55,6 +55,10 @@ default=INFO
 #CoordCoverageExtensionChooser=DEBUG
 #SimpleCoverageExtensionChooser=DEBUG
 #IdealInfoProvider=TRACE
+#ExtendersLogic=DEBUG
+#LongReadsRNAExtensionChooser=DEBUG
+#MultiExtender=DEBUG
+
 
 #BWAPairInfo=TRACE
 #LongReadMapper=TRACE

assembler/configs/debruijn/meta_mode.info

@@ -2,6 +2,8 @@ mode    meta
 
 ; two-step pipeline
 two_step_rr true
+min_edge_length_for_is_count 900
+
 ; enables/disables usage of intermediate contigs in two-step pipeline
 use_intermediate_contigs true
 

assembler/configs/debruijn/pe_params.info

@@ -167,5 +167,13 @@ long_reads {
         min_significant_overlap 200
     }
 
+    rna_long_reads {
+        filtering   0.1
+        weight_priority    1.1
+        unique_edge_priority 2.0
+        min_significant_overlap 0
+    }
+
+
 }
 }