Spades что это за программа

SPAdes 3.12.0 Manual

1. About SPAdes

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.12.0 was released under GPLv2 on May 14, 2018 and can be downloaded from http://cab.spbu.ru/software/spades/.

1.1 Supported data types

The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.

Version 3.12.0 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.

In addition, we provide several stand-alone binaries with relatively simple command-line interface: k-mer counting ( spades-kmercounter ), assembly graph construction ( spades-gbuilder ) and long read to graph aligner ( spades-gmapper ). To learn options of these tools you can either run them without any parameters or read this section.

1.2 SPAdes pipeline

We recommend to run SPAdes with BayesHammer/IonHammer to obtain high-quality assemblies. However, if you use your own read correction tool, it is possible to turn error correction module off. It is also possible to use only the read error correction stage, if you wish to use another assembler. See the SPAdes options section.

1.3 SPAdes’ performance

We ran SPAdes with default parameters using 16 threads on a server with Intel Xeon 2.27GHz processors. The results for both datasets are pretty similar: BayesHammer runs in less than half an hour and takes up to 8Gb of RAM, assembly takes about 10 minutes and 9Gb of RAM (see notes below), MismatchCorrector runs for slightly more than 10 minutes and requires less than 2Gb of RAM. All modules also require additional disk space for storing results (corrected reads, contigs, etc) and temporary files. See the table below for more precise values.

2. Installation

SPAdes requires a 64-bit Linux system or Mac OS and Python (supported versions are Python2: 2.4–2.7, and Python3: 3.2 and higher) to be pre-installed on it. To obtain SPAdes you can either download binaries or download source code and compile it yourself.

2.1 Downloading SPAdes Linux binaries

To download SPAdes Linux binaries and extract them, go to the directory in which you wish SPAdes to be installed and run:

SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the PATH variable.

2.2 Downloading SPAdes binaries for Mac

To obtain SPAdes binaries for Mac, go to the directory in which you wish SPAdes to be installed and run:

Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the PATH variable.

2.3 Downloading and compiling SPAdes source code

If you meet these requirements, you can download the SPAdes source code:

and build it with the following script:

2.4 Verifying your installation

For testing purposes, SPAdes comes with a toy data set (reads that align to first 1000 bp of E. coli). To try SPAdes on this data set, run:

If you added SPAdes installation directory to the PATH variable, you can run: For the simplicity we further assume that SPAdes installation directory is added to the PATH variable.

If the installation is successful, you will find the following information at the end of the log:

3. Running SPAdes

3.1 SPAdes input

SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.

Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.

SPAdes supports mate-pair only assembly. However, we recommend to use only high-quality mate-pair libraries in this case (e.g. that do not have a paired-end part). We tested mate-pair only pipeline using Illumina Nextera mate-pairs. See more here.

Current version SPAdes also supports Lucigen NxSeq® Long Mate Pair libraries, which always have forward-reverse orientation. If you wish to use Lucigen NxSeq® Long Mate Pair reads, you will need Python regex library to be pre-installed on your machine. You can install it with Python pip-installer: or with the Easy Install Python module:

Read-pair libraries

By using command line interface, you can specify up to nine different paired-end libraries, up to nine mate-pair libraries and also up to nine high-quality mate-pair ones. If you wish to use more, you can use YAML data set file. We further refer to paired-end and mate-pair libraries simply as to read-pair libraries.

By default, SPAdes assumes that paired-end and high-quality mate-pair reads have forward-reverse (fr) orientation and usual mate-pairs have reverse-forward (rf) orientation. However, different orientations can be set for any library by using SPAdes options.

To distinguish reads in pairs we refer to them as left and right reads. For forward-reverse orientation, the forward reads correspond to the left reads and the reverse reads, to the right. Similarly, in reverse-forward orientation left and right reads correspond to reverse and forward reads, respectively, etc.

If adapter and/or quality trimming software has been used prior to assembly, files with the orphan reads can be provided as «single read files» for the corresponding read-pair library.

If you have merged some of the reads from your paired-end (not mate-pair or high-quality mate-pair) library (using tools s.a. BBMerge or STORM), you should provide the file with resulting reads as a «merged read file» for the corresponding library.
Note that non-empty files with the remaining unmerged left/right reads (separate or interlaced) must be provided for the same library (for SPAdes to correctly detect the original read length).

In an unlikely case some of the reads from your mate-pair (or high-quality mate-pair) library are «merged», you should provide the resulting reads as a SEPARATE single-read library.

Unpaired (single-read) libraries

By using command line interface, you can specify up to nine different single-read libraries. To input more libraries, you can use YAML data set file.

Single librairies are assumed to have high quality and a reasonable coverage. For example, you can provide PacBio CCS reads as a single-read library.

Note, that you should not specify PacBio CLR, Sanger reads or additional contigs as single-read libraries, each of them has a separate option.

PacBio and Oxford Nanopore reads

SPAdes can take as an input an unlimited number of PacBio and Oxford Nanopore libraries.

PacBio CLR and Oxford Nanopore reads are used for hybrid assemblies (e.g. with Illumina or IonTorrent). There is no need to pre-correct this kind of data. SPAdes will use PacBio CLR and Oxford Nanopore reads for gap closure and repeat resolution.

PacBio CCS/Reads of Insert reads or pre-corrected (using third-party software) PacBio CLR / Oxford Nanopore reads can be simply provided as single reads to SPAdes.

Additional contigs

Note, that SPAdes does not perform assembly using genomes of closely-related species. Only contigs of the same genome should be specified.

3.2 SPAdes command line options

To run SPAdes from the command line, type Note that we assume that SPAdes installation directory is added to the PATH variable (provide full path to SPAdes executable otherwise: /spades.py ).

Basic options

-o
Specify the output directory. Required option.

—sc
This flag is required for MDA (single-cell) data.

—plasmid (same as plasmidspades.py )
This flag is required when assembling only plasmids from WGS data sets (runs plasmidSPAdes, see paper for the algorithm details). Note, that plasmidSPAdes is not compatible with metaSPAdes and single-cell mode. Additionally, we do not recommend to run plasmidSPAdes on more than one library. See section 3.6 for plasmidSPAdes output details.

—rna (same as rnaspades.py )
This flag should be used when assembling RNA-Seq data sets (runs rnaSPAdes). To learn more, see rnaSPAdes manual.

—iontorrent
This flag is required when assembling IonTorrent data. Allows BAM files as input. Carefully read section 3.3 before using this option.

—test
Runs SPAdes on the toy data set; see section 2.4.

Pipeline options

—only-error-correction
Performs read error correction only.

—only-assembler
Runs assembly module only.

—careful
Tries to reduce the number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes). This option is recommended only for assembly of small genomes. We strongly recommend not to use it for large and medium-size eukaryotic genomes. Note, that this options is is not supported by metaSPAdes and rnaSPAdes.

YAML file should look like this:

Advanced options

—tmp-dir
Set directory for temporary files from read error correction. The default value is /corrected/tmp

—cov-cutoff
Read coverage cutoff value. Must be a positive float value, or ‘auto’, or ‘off’. Default value is ‘off’. When set to ‘auto’ SPAdes automatically computes coverage threshold using conservative strategy. Note, that this option is not supported by metaSPAdes.

—phred-offset
PHRED quality offset for the input reads, can be either 33 or 64. It will be auto-detected if it is not specified.

Examples

To test the toy data set, you can also run the following command from the SPAdes bin directory:

If you have your library separated into several pairs of files, for example:

make sure that corresponding files are given in the same order:

Files with interlacing paired-end reads or files with unpaired reads can be specified in any order with one file per option, for example:

make sure that files corresponding to each library are grouped together:

If you have IonTorrent unpaired reads, PacBio CLR and additional reliable contigs:

run SPAdes with the following command:

If a single-read library is splitted into several files:

specify them as one library:

All options for specifying input data can be mixed if needed, but make sure that files for each library are grouped and files with left and right paired reads are listed in the same order.

3.3 Assembling IonTorrent reads

Only FASTQ or BAM files are supported as input.

To correct and assemble the reads:

Multi-cell data set with read lengths 2 x 250

Do not turn off SPAdes error correction (BayesHammer module), which is included in SPAdes default pipeline.

By default we suggest to increase k-mer lengths in increments of 22 until the k-mer length reaches 127. The exact length of the k-mer depends on the coverage: k-mer length of 127 corresponds to 50x k-mer coverage and higher. For read length 250bp SPAdes automatically chooses K values equal to 21, 33, 55, 77, 99, 127.

We recommend you to check the SPAdes log file at the end of the each iteration to control the average coverage of the contigs.

For reads corrected prior to running the assembler:

To correct and assemble the reads:

Single-cell data set with read lengths 2 x 150 or 2 x 250

The default k-mer lengths are recommended. For single-cell data sets SPAdes selects k-mer sizes 21, 33 and 55.

However, it might be tricky to fully utilize the advantages of long reads you have. Consider contacting us for more information and to discuss assembly strategy.

3.5 SPAdes output

Contigs/scaffolds names in SPAdes output FASTA files have the following format:
>NODE_3_length_237403_cov_243.207
Here 3 is the number of the contig/scaffold, 237403 is the sequence length in nucleotides and 243.207 is the k-mer coverage for the last (largest) k value used. Note that the k-mer coverage is always lower than the read (per-base) coverage.

In general, SPAdes uses two techniques for joining contigs into scaffolds. First one relies on read pairs and tries to estimate the size of the gap separating contigs. The second one relies on the assembly graph: e.g. if two contigs are separated by a complex tandem repeat, that cannot be resolved exactly, contigs are joined into scaffold with a fixed gap size of 100 bp. Contigs produced by SPAdes do not contain N symbols.

To view FASTG and GFA files we recommend to use Bandage visualization tool. Note that sequences stored in assembly_graph.fastg correspond to contigs before repeat resolution (edges of the assembly graph). Paths corresponding to contigs after repeat resolution (scaffolding) are stored in contigs.paths ( scaffolds.paths ) in the format accepted by Bandage (see Bandage wiki for details). The example is given below.

Let the contig with the name NODE_5_length_100000_cov_215.651 consist of the following edges of the assembly graph:

Then, contigs.paths will contain the following record:

The full list of content is presented below:

3.6 plasmidSPAdes output

3.7 Assembly evaluation

QUAST may be used to generate summary statistics (N50, maximum contig length, GC %, # genes found in a reference list or with built-in gene finding tools, etc.) for a single assembly. It may also be used to compare statistics for multiple assemblies of the same data set (e.g., SPAdes run with different parameters, or several different assemblers).

4. Stand-alone binaries released within SPAdes package

4.1 k-mer counting

Synopsis: spades-kmercount [OPTION. ]

4.2 Graph construction

Graph construction tool spades-gbuilder has two mandatory options: dataset description file in YAML format and an output file name.

Synopsis: spades-gbuilder [-k ] [-t ] [-tmpdir ] [-b ] [-unitigs|-fastg|-gfa|-spades]

Additional options are:

-k
k-mer length used for construction (must be odd)

-t
number of threads

-tmpdir
scratch directory to use

-b
sorting buffer size (per thread, in bytes)

-unitigs
k-mer length used for construction (must be odd)

-fastg
output graph in FASTG format

-gfa
output graph in GFA1 format

-spades
output graph in SPAdes internal format

4.3 Long read to graph aligner

A tool for aligning long reads to the graph spades-gmapper has three mandatory options: dataset description file in YAML format, graph file in GFA format and an output file name.

Synopsis: spades-gmapper [-k ] [-t ] [-tmpdir ]

Additional options are:

-k
k-mer length that was used for graph construction

-t
number of threads

-tmpdir
scratch directory to use

5. Citation

If you use SPAdes in your research, please include Nurk, Bankevich et al., 2013 in your reference list. You may also add Bankevich, Nurk et al., 2012 instead.

If you use PacBio or Nanopore reads, you may also cite Antipov et al., 2015. If you use multiple paired-end and/or mate-pair libraries you may also cite papers describing SPAdes repeat resolution algorithms Prjibelski et al., 2014 and Vasilinetc et al., 2015. If you use plasmidSPAdes please cite Antipov et al., 2016.

For the information about dipSPAdes and truSPAdes papers see dipSPAdes manual and truSPAdes manual respectively.

Источник

Что такое spades.exe? Это безопасно или вирус? Как удалить или исправить это

Что такое spades.exe?

spades.exe это исполняемый файл, который является частью 1000 Лучшие игры разработанный Cosmi Corporation, Версия программного обеспечения для Windows 95 95: 1.0.0.0 обычно 457348 в байтах, но у вас может отличаться версия.

Spades.exe безопасный, или это вирус или вредоносная программа?

Первое, что поможет вам определить, является ли тот или иной файл законным процессом Windows или вирусом, это местоположение самого исполняемого файла. Например, для spades.exe его путь будет примерно таким: C: \ Program Files \ Cosmi Corporation \ 1000 Best Games \ spades.exe

Если статус процесса «Проверенная подписывающая сторона» указан как «Невозможно проверить», вам следует взглянуть на процесс. Не все хорошие процессы Windows имеют метку проверенной подписи, но ни один из плохих.

Самые важные факты о spades.exe:

Если у вас возникли какие-либо трудности с этим исполняемым файлом, перед удалением spades.exe вы должны определить, заслуживает ли он доверия. Для этого найдите этот процесс в диспетчере задач.

Найти его местоположение и сравнить размер и т. Д. С приведенными выше фактами

Если вы подозреваете, что можете быть заражены вирусом, вы должны немедленно попытаться это исправить. Чтобы удалить вирус spades.exe, необходимо скачайте и установите приложение полной безопасности, как это, Обратите внимание, что не все инструменты могут обнаружить все типы вредоносных программ, поэтому вам может потребоваться попробовать несколько вариантов, прежде чем вы добьетесь успеха.

Могу ли я удалить или удалить spades.exe?

Не следует удалять безопасный исполняемый файл без уважительной причины, так как это может повлиять на производительность любых связанных программ, использующих этот файл. Не забывайте регулярно обновлять программное обеспечение и программы, чтобы избежать будущих проблем, вызванных поврежденными файлами. Что касается проблем с функциональностью программного обеспечения, проверяйте обновления драйверов и программного обеспечения чаще, чтобы избежать или вообще не возникало таких проблем.

Однако, если это не вирус, и вам необходимо удалить spades.exe, вы можете удалить 1000 Best Games со своего компьютера, используя его деинсталлятор. Если вы не можете найти его деинсталлятор, вам может понадобиться удалить 1000 Best Games, чтобы полностью удалить spades.exe. Вы можете использовать функцию «Установка и удаление программ» на панели управления Windows.

Распространенные сообщения об ошибках в spades.exe

Наиболее распространенные ошибки spades.exe, которые могут возникнуть:

• «Ошибка приложения spades.exe.»
• «Ошибка spades.exe».
• «Возникла ошибка в приложении spades.exe. Приложение будет закрыто. Приносим извинения за неудобства».
• «spades.exe не является допустимым приложением Win32».
• «spades.exe не запущен».
• «spades.exe не найден».
• «Не удается найти spades.exe».
• «Ошибка запуска программы: spades.exe.»
• «Неверный путь к приложению: spades.exe.»

Как исправить spades.exe

Если у вас возникла более серьезная проблема, постарайтесь запомнить последнее, что вы сделали, или последнее, что вы установили перед проблемой. Использовать resmon Команда для определения процессов, вызывающих вашу проблему. Даже в случае серьезных проблем вместо переустановки Windows вы должны попытаться восстановить вашу установку или, в случае Windows 8, выполнив команду DISM.exe / Online / Очистка-изображение / Восстановить здоровье, Это позволяет восстановить операционную систему без потери данных.

Чтобы помочь вам проанализировать процесс spades.exe на вашем компьютере, вам могут пригодиться следующие программы: Менеджер задач безопасности отображает все запущенные задачи Windows, включая встроенные скрытые процессы, такие как мониторинг клавиатуры и браузера или записи автозапуска. Единый рейтинг риска безопасности указывает на вероятность того, что это шпионское ПО, вредоносное ПО или потенциальный троянский конь. Это антивирус обнаруживает и удаляет со своего жесткого диска шпионское и рекламное ПО, трояны, кейлоггеры, вредоносное ПО и трекеры.

Обновлен декабрь 2021:

Мы рекомендуем вам попробовать этот новый инструмент. Он исправляет множество компьютерных ошибок, а также защищает от таких вещей, как потеря файлов, вредоносное ПО, сбои оборудования и оптимизирует ваш компьютер для максимальной производительности. Это исправило наш компьютер быстрее, чем делать это вручную:

Загрузите или переустановите spades.exe

Вход в музей Мадам Тюссо не рекомендуется загружать заменяемые exe-файлы с любых сайтов загрузки, так как они могут содержать вирусы и т. д. Если вам нужно скачать или переустановить spades.exe, мы рекомендуем переустановить основное приложение, связанное с ним. 1000 Лучшие игры.

Лучшие веб-игры 30 (которые мы можем вспомнить)

Информация об операционной системе

Ошибки spades.exe могут появляться в любых из нижеперечисленных операционных систем Microsoft Windows:

Источник

Center for Algorithmic Biotechnology

CAB SPbU

SPAdes

SPAdes

Content

SPAdes 3.15.3

It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines.

Manuals and support

Note, that SPAdes binaries may not work on new Linux kernels.

Subscribe for updates

For the benchmarks we used:

214bp (Illumina Genome Analyzer IIx)

More datasets as well as reference genomes are available here.

E. coli K-12 MG1655 reference length is 4639675 bp with 4324 annotated genes. S. aureus USA300 FPR3757 (chromosome and three plasmids) reference length is 2917469 bp with 2622 annotated genes.

Only contigs of 500 bp and longer were taken in consideration. Tables were obtained using QUAST 4.6.3.

A5 and CLC 3.22.55708 were run with default parameters. ABySS 1.3.5, EULER-SR 2.0.1, Ray 2.2.0, SOAPdenovo 2.04, Velvet 1.2.07, and E+V-SC were run with vertex size 55. IDBA-UD 1.1.0 was run in its default iterative mode.

Acknowledgements

This work was supported by the Russian Science Foundation (grant 14-50-00069). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project.

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