.gitignore

+.settings
+.metadata/*
+.idea
+stats/*
+RemoteSystemsTempFiles/*
+~*
+*~
+*.exe
+*.exe.stackdump
+gmon.out
+CMakeFiles
+CMakeCache.txt
+cmake_install.cmake
+assembler/src/tools/quality/results*

README

-SPAdes
-Genome assembler for single-cell and isolates data sets
-Version: see VERSION
-
-Developed in Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University.
-Developed in Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences.
-
-Current SPAdes contributors:
-
-    Dmitry Antipov,
-    Anton Bankevich,
-    Elena Bushmanova,
-    Vasisliy Ershov,
-    Yuriy Gorshkov,
-    Alexey Gurevich,
-    Anton Korobeynikov,
-    Sergey Nurk,
-    Andrey Prjibelski,
-    Ivan Tolstoganov,
-    Alla Lapidus and
-    Pavel Pevzner
-
-Also contributed:
-
-    Max Alekseyev,
-    Mikhail Dvorkin,
-    Alexander Kulikov,
-    Valery Lesin,
-    Dmitriy Meleshko,
-    Sergey Nikolenko,
-    Son Pham,
-    Alexey Pyshkin,
-    Yana Safonova,
-    Vladislav Saveliev,
-    Alexander Sirotkin,
-    Yakov Sirotkin,
-    Artem Tarasov,
-    Glenn Tesler,
-    Irina Vasilinetc,
-    Nikolay Vyahhi
-
-Installation instructions and manual can be found on the website:
-http://cab.spbu.ru/software/spades/
-
-Address for communication: spades.support@cab.spbu.ru
-
-References:
-
-Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin,
-Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler,
-Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
-Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021
-
-Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov,
-Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin,
-Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken,
-Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner.
-Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes
-in Computer Science 7821 (2013), pp. 158-170. doi:10.1007/978-3-642-37195-0_13
-

VERSION

-3.12.0

assembler/.gitignore

+bin/
+build/
+build_spades/
+logs/
+output/
+spades_output/
+spades_test/
+spades_test_truspades/
+teamcity_precompiled/
+CMakeFiles/
+scripts/
+share/
+*.launch
+*.ebwt
+*.pyc
+*.pyo
+*.class
+tags
+.DS_Store
+._.DS_Store
+spades_config.info
+bh_config.info
+bin
+build_spades
+share

LICENSE → assembler/LICENSE

 SPADES: SAINT-PETERSBURG GENOME ASSEMBLER
-Copyright (c) 2015-2018 Saint Petersburg State University
+Copyright (c) 2015-2019 Saint Petersburg State University
 Copyright (c) 2011-2014 Saint Petersburg Academic University
 
 SPAdes is free software; you can redistribute it and/or modify
@@ -17,17 +17,26 @@ with this program; if not, write to the Free Software Foundation, Inc.,
 
 -------------------------------------------------------------------------------
 
+SPAdes
+Genome assembler for single-cell and isolates data sets
+Version: see VERSION
+
+Developed in Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University.
+Developed in Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences.
+
 Current SPAdes contributors:
 
     Dmitry Antipov,
-    Anton Bankevich,
     Elena Bushmanova,
     Vasisliy Ershov,
     Yuriy Gorshkov,
     Alexey Gurevich,
     Anton Korobeynikov,
+    Olga Kunyavskaya,
+    Dmitriy Meleshko,
     Sergey Nurk,
     Andrey Prjibelski,
+    Alexander Shlemov,
     Ivan Tolstoganov,
     Alla Lapidus and
     Pavel Pevzner
@@ -35,10 +44,10 @@ Current SPAdes contributors:
 Also contributed:
 
     Max Alekseyev,
+    Anton Bankevich,
     Mikhail Dvorkin,
     Alexander Kulikov,
     Valery Lesin,
-    Dmitriy Meleshko,
     Sergey Nikolenko,
     Son Pham,
     Alexey Pyshkin,
@@ -51,9 +60,10 @@ Also contributed:
     Irina Vasilinetc,
     Nikolay Vyahhi
 
-Contacts:
+Installation instructions and manual can be found on the website:
 http://cab.spbu.ru/software/spades/
-    spades.support@cab.spbu.ru
+
+Address for communication: spades.support@cab.spbu.ru
 
 References:
 

assembler/VERSION

+3.13.1

changelog.html → assembler/changelog.html

@@ -3,6 +3,26 @@
 
 <h2>SPAdes Genome Assembler changelog</h2>
 
+<h3>SPAdes 3.13.1, 11 April 2019</h3>
+
+<p>CHANGE: Removed BayesHammer from rnaSPAdes pipeline.</p>
+
+<p>CHANGE: Improved rnaSPAdes performance on large datasets.</p>
+
+<p>FIX: Failure in contig output in rnaSPAdes.</p>
+
+<h3>SPAdes 3.13.0, 11 October 2018</h3>
+
+<p>CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected automatically based on read length.</p>
+
+<p>CHANGE: Added manual as README.md in markdown format for github.</p>
+
+<p>FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.</p>
+
+<p>FIX: Assert for path.length() > 0 in rnaSPAdes. </p>
+
+<p>FIX: CQF and k-mer counting. </p>
+
 <h3>SPAdes 3.12.0, 14 May 2018</h3>
 
 <p>NEW: Support for merged paired-end reads.</p>

assembler/changer_of_K.py

+#!/usr/bin/env python
+
+import os
+import shutil
+import sys
+import getopt
+import glob
+
+import spades_init
+
+spades_init.init()
+spades_home = spades_init.spades_home
+
+import support
+from process_cfg import *
+
+def prepare_config(filename, K):
+    subst_dict = dict()
+    subst_dict["K"] = K
+    substitute_params(filename, subst_dict)
+
+
+if len(sys.argv) != 2:
+    print ("Usage: " + sys.argv[0] + " K")
+    exit(0)
+
+config = "configs/debruijn/config.info"
+K = sys.argv[1]
+print ("Changing to K = " + K)
+prepare_config(config, K)
+    
+
+

assembler/compare_saves.sh

+#!/bin/bash
+
+for file in $(ls $1/saves/)
+do 
+	echo $file
+	cmp  $1/saves/$(basename $file) $2/saves/$(basename $file)
+done
+

assembler/configs/.gitignore

+debruijn/config.info
+debruijn/simplification.info
+debruijn/distance_estimation.info
+debruijn/detail_info_printer.info
+debruijn/log.properties
+debruijn/path_extend/pe_config.info
+debruijn/path_extend/pe_params.info
+debruijn/path_extend/pe_libs.info
+debruijn/construction.info
+hammer/config.info
+_generic/

configs/debruijn/config.info → assembler/configs/debruijn/config.info

@@ -175,3 +175,12 @@ bwa_aligner
 flanking_range 55
 series_analysis ""
 save_gp false
+
+ss_coverage_splitter {
+    enabled           false
+    bin_size          50
+    min_edge_len      200
+    min_edge_coverage 5
+    min_flanking_coverage 2
+    coverage_margin   5
+}