shasta | De novo assembly from Oxford Nanopore reads | Genomics library

 by   chanzuckerberg C++ Version: 0.9.0 License: Non-SPDX

kandi X-RAY | shasta Summary

kandi X-RAY | shasta Summary

shasta is a C++ library typically used in Artificial Intelligence, Genomics applications. shasta has no bugs, it has no vulnerabilities and it has low support. However shasta has a Non-SPDX License. You can download it from GitHub.

See Shafin et al., Nature Biotechnology 2020 for error analysis of the Shasta assembler and more. Reads from this paper are available here. The assembly results are here. Here is a QUAST analysis of a Shasta assembly of CHM13 and a comparison with other assemblers. Requests for help: please file GitHub issues to report problems, request help, or ask questions. Please keep each issue on a single topic when possible. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input.
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            kandi-support Support

              shasta has a low active ecosystem.
              It has 248 star(s) with 43 fork(s). There are 24 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 3 open issues and 96 have been closed. On average issues are closed in 59 days. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of shasta is 0.9.0

            kandi-Quality Quality

              shasta has no bugs reported.

            kandi-Security Security

              shasta has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              shasta has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              shasta releases are available to install and integrate.

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            shasta Key Features

            No Key Features are available at this moment for shasta.

            shasta Examples and Code Snippets

            No Code Snippets are available at this moment for shasta.

            Community Discussions

            QUESTION

            Gsub command to replace all spaces with a comma and space, (", "), except after certain words with R
            Asked 2021-Jun-05 at 00:29

            I have a data.frame with a column containing California counties in each cell separated by a space. I would like to add a comma and space after each one, however I can't just gsub every space into a comma and space, (i.e. gsub("\s",",\s",text)), as some counties in California have two names, (e.g. Los Angeles, San Francisco, etc.)

            Fortunately, the two-word counties all have common first words so I'd like to write a gsub that preserves the space in those counties without adding a comma. I've attached example data as well as what I'd like the final form to look like. For instance, with this data, I'd like to add a comma and space except after "El", "San" and "Del".

            Example data:

            ...

            ANSWER

            Answered 2021-Jun-05 at 00:29

            Given that you know you are only looking for California counties, one "easy" way is just to replace only spaces that occur after a California county. To get that regex, I just concatenated the CA county names together with | and added a space. The gsub will replace any county name followed by a space with the same county name (\\1), a comma, and a space.

            Source https://stackoverflow.com/questions/67845153

            QUESTION

            TronWeb UnhandledPromiseRejectionWarning: TypeError: e.forEach is not a function
            Asked 2021-Mar-25 at 20:50

            I'm triyng build interfacing with simple tron smartcontract with front end but i cant! Here is problem:

            ...

            ANSWER

            Answered 2021-Mar-25 at 20:49

            Try

            instance = await tronWeb.contract().at(trc20ContractAddress)

            Source https://stackoverflow.com/questions/66797992

            QUESTION

            Create dictionary from a nested list
            Asked 2021-Jan-14 at 23:31

            I have a nested list that looks like this:

            ...

            ANSWER

            Answered 2021-Jan-14 at 23:31

            QUESTION

            Extract elements from list in Python to create nested list
            Asked 2021-Jan-14 at 21:52

            I have a list such as this (this is pulled from some html texts using bs4):

            ...

            ANSWER

            Answered 2021-Jan-14 at 21:28

            What about something like:

            Source https://stackoverflow.com/questions/65727119

            QUESTION

            How to add null in text input if user does not enter any address
            Asked 2020-Nov-17 at 11:57
                function deposit(address payable referrer) public payable whenNotPaused
                {  
                
                }
            
            ...

            ANSWER

            Answered 2020-Nov-17 at 11:57

            I'm trying to understand your question.
            Are you want to use default parameters?

            Well, Solidity does not support default parameters, but it is on their roadmap (see https://github.com/ethereum/solidity/issues/232). To work around this, just use function overloading:

            Source https://stackoverflow.com/questions/64742970

            QUESTION

            R duplicate rows based on the elements in a string column
            Asked 2020-Jul-20 at 08:48

            I have a more or less specific question that probably pertains to loops in R. I have a dataframe:

            ...

            ANSWER

            Answered 2020-Jul-20 at 08:48

            You can use str_extract_all to extract all the states and unnest to duplicate rows such that each state is in a separate row. There is an inbuilt constant state.name which have the state names of US which can be used here to create pattern.

            Source https://stackoverflow.com/questions/62991663

            QUESTION

            Exclude rows based on condition from two columns
            Asked 2020-Jun-25 at 10:43

            My question is very similar to this one, except that I want to exclude all columns that have a unique value in a column. If we assume that to be the input.

            ...

            ANSWER

            Answered 2020-Jun-25 at 10:43

            QUESTION

            Always returning empty array of arrays, although it's showing successful transaction on Shasta Network
            Asked 2020-Apr-29 at 10:09

            I'm trying to get back all the struct type records from my solidity contract function please see the below solidity contract code snippet

            ...

            ANSWER

            Answered 2020-Apr-12 at 03:24

            In ABI, any return value of a struct type will be interpreted as tuple. In your case, its type is tuple[].

            The library has no clue what's your tuple is, how long it is, what's the type.

            You should parse the return data by hand.

            Source https://stackoverflow.com/questions/61107744

            QUESTION

            TronBox compile issue
            Asked 2019-Dec-11 at 09:05
            • I've installed the latest tronbox (2.7.5) using npm
            • Created a new project using command tronbox init
            • In file tronbox.js i've update the compiler version to 0.4.25 (see the file below).
            • When compiling using command tronbox compile --compile-all --reset I'm getting:

            Windows error:

            And then the following message in my terminal:

            ...

            ANSWER

            Answered 2019-Dec-11 at 09:05

            This seems like a regression bug in tronbox 2.7.4 and 2.7.5 since when I use tronbox 2.5.2 everything works smoothly.

            Source https://stackoverflow.com/questions/59256712

            QUESTION

            How to obtain ratio of column X over column Y in SQLlite?
            Asked 2019-Mar-27 at 00:04

            I am supposed to obtain the following result: Demographics: Ratio of Men and Women Write a query that shows the ratio of men and women (pop_male divided by pop_female) over the age of 18 by county in 2018. Order the results from the most female to the most male counties.

            ...

            ANSWER

            Answered 2019-Mar-26 at 23:35

            Don't want to override the SQLRaptor's helpful response in comments, but for the sake of completeness :)

            SQL treats integer division as integer, therefore truncating it. To avoid that -- cast at least one of the values to a floating point data type (e.g. REAL or FLOAT for SQLite -- check the manual on data types here: https://www.sqlite.org/datatype3.html)

            Source https://stackoverflow.com/questions/55367362

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install shasta

            You can download it from GitHub.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            CLONE
          • HTTPS

            https://github.com/chanzuckerberg/shasta.git

          • CLI

            gh repo clone chanzuckerberg/shasta

          • sshUrl

            git@github.com:chanzuckerberg/shasta.git

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