nanopolish | Signal-level algorithms for MinION data | Genomics library

 by   jts C++ Version: v0.14.0 License: MIT

kandi X-RAY | nanopolish Summary

kandi X-RAY | nanopolish Summary

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

Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).
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              nanopolish has a low active ecosystem.
              It has 487 star(s) with 155 fork(s). There are 38 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 67 open issues and 891 have been closed. On average issues are closed in 44 days. There are 8 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of nanopolish is v0.14.0

            kandi-Quality Quality

              nanopolish has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              nanopolish is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              nanopolish releases are not available. You will need to build from source code and install.
              Installation instructions are not available. Examples and code snippets are available.

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            nanopolish Key Features

            No Key Features are available at this moment for nanopolish.

            nanopolish Examples and Code Snippets

            No Code Snippets are available at this moment for nanopolish.

            Community Discussions

            QUESTION

            snakemake - replacing command line parameters with wildcards by cluster profile
            Asked 2021-Jun-10 at 07:54

            I am writing a snakemake pipeline to eventually identify corona virus variants.

            Below is a minimal example with three steps:

            ...

            ANSWER

            Answered 2021-Jun-10 at 07:54

            I think the problem is that rule catFasta doesn't contain the wildcard barcode. If you think about it, what job name would you expect in {wildcards.barcode}.{rule}.{jobid}?

            Maybe a solution could be to add to each rule a jobname parameter that could be {barcode} for guppyplex and minion and 'all_barcodes' for catFasta. Then use --jobname "{params.jobname}.{rule}.{jobid}"

            Source https://stackoverflow.com/questions/67906871

            QUESTION

            snakemake - define input for aggregate rule without wildcards
            Asked 2021-Jun-08 at 15:40

            I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex and artic minion.

            The snakemake that I wrote has the following steps:

            1. zip all the fastq files for all barcodes (rule zipFq)
            2. perform read filtering with guppyplex (rule guppyplex)
            3. call the artic minion pipeline (rule minion)
            4. move the stderr and stdout from qsub to a folder under the working directory (rule mvQsubLogs)

            Below is the snakemake that I wrote so far, which works

            ...

            ANSWER

            Answered 2021-Jun-08 at 15:40

            The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

            Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

            First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

            It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

            Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

            However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

            Edit: Dummy test example:

            Source https://stackoverflow.com/questions/67805295

            QUESTION

            ChildIOException: error in snake make after running flye
            Asked 2019-Nov-11 at 21:08

            So I have an issue when I run other programs after I ran flye in my snakemake pipeline. This is because the output from flye is a directory. My rules are as followd:

            ...

            ANSWER

            Answered 2019-Nov-11 at 21:08

            (I think) The problem lies somewhere else in your code.

            You have defined two rules, the first that outputs directory assembled, the second that outputs assembled/assembly.fasta. Since the output of the second rule is always at least the directory assembled, Snakemake complains. You can solve it by using the directory as input:

            Source https://stackoverflow.com/questions/58808354

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

            Vulnerabilities

            No vulnerabilities reported

            Install nanopolish

            You can download it from GitHub.

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            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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            https://github.com/jts/nanopolish.git

          • CLI

            gh repo clone jts/nanopolish

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            git@github.com:jts/nanopolish.git

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