graphmap | highly sensitive and accurate mapper | Genomics library

 by   isovic C++ Version: v0.3.0 License: MIT

kandi X-RAY | graphmap Summary

kandi X-RAY | graphmap Summary

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

GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers. GraphMap was also designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore. This is an especially important feature for technologies where the error rates and error profiles can vary widely across, or even within, sequencing runs. The GraphMap algorithm is structured to achieve high-sensitivity and speed using a five-stage read-funneling approach. In stage I, GraphMap uses a novel adaptation of gapped spaced seeds to efficiently reduce the search space and get seed hits as a form of coarse alignment. These are then refined in stage II using graph-based vertex-centric processing of seeds to efficiently construct alignment anchors. GraphMap then chains anchors using a kmer version of longest common subsequence (LCSk) construction (stage III), refines alignments by chaining anchors in the anchored mode or with a form of L1 linear regression in the semiglobal alignment mode (stage IV) and finally evaluates the remaining candidates to select the best location to reconstruct a final alignment (stage V). GraphMap computes a BLAST-like E-value as well as a mapping quality for its alignments. Evaluation on MinION sequencing datasets against short and long-read mappers indicates that GraphMap increases mapping sensitivity by at least 15-80%. GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM), precise detection of structural variants from 100bp to 4kbp in length and species and strain-specific identification of pathogens using MinION reads. Further details about the algorithm, comparison with other mappers and usage applications can be found in the preprint of our paper: Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap. Nanopore sequencing data of E. Coli UTI89 generated in-house and used in the paper now available on ENA: PRJEB9557.
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            kandi-support Support

              graphmap has a low active ecosystem.
              It has 159 star(s) with 43 fork(s). There are 26 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 36 open issues and 60 have been closed. On average issues are closed in 43 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of graphmap is v0.3.0

            kandi-Quality Quality

              graphmap has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              graphmap 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

              graphmap releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            graphmap Key Features

            No Key Features are available at this moment for graphmap.

            graphmap Examples and Code Snippets

            No Code Snippets are available at this moment for graphmap.

            Community Discussions

            QUESTION

            zlib.h:34:19: fatal error: zconf.h: No such file or directory #include "zconf.h"
            Asked 2021-May-21 at 08:54

            There are quite some posts about this error, but I was not able to solve it, I hope you can come up with the solution. I am on a Ubuntu machine.

            ~/graphmap2$

            In this folder, I downloaded zlib. You can see the picture

            After some Googling, I also noticed that there is no -lz parameter, so I also added that manually as you can see below

            However, I still get the same error as when none of the above were done.

            Might it be that the path to zlib is not clear for the compiler? However, I installed it in this same folder.

            The make file looks like the below:

            ...

            ANSWER

            Answered 2021-May-21 at 03:35

            Seems compiler is not able to find the file in the includes path you mentioned.
            First check if zconf.h file is available on your machine and get that location. If the file is available then just give the path of the file to the compiler using -I option.

            Source https://stackoverflow.com/questions/67621721

            QUESTION

            How to calculate the betweenness centrality with weights
            Asked 2020-Nov-09 at 16:28

            I'm trying to calculate the betweenness centrality of a city street network, using the Edge length property as weight, but it doesn't seem to work.

            When I run without weights it gives the following results:

            ...

            ANSWER

            Answered 2020-Nov-09 at 16:28

            Well, that's awkward, turns out the code is right, my graph was somehow wrong, I regenerated it and it has worked.

            Edit 1

            After seeing the time and amount of memory it takes to load the graph, I was able to find the problem, after I made some operations on the nodes, I was inserting them in the same graph, instead of a new one.

            Edit 2

            The way the betweenness with weights function is invoked is wrong, the right way would be:

            Source https://stackoverflow.com/questions/64709107

            QUESTION

            Create a Petgraph graph from a Vec<(String, String)> loaded from JSON
            Asked 2020-Jan-28 at 22:58

            I'm trying to create a petgraph Graph from JSON data. The JSON contains the edges of the graph, the key represents the starting vertex and the value is a list of adjacent vertices. It's possible to generate a graph with a vector of edges.

            I managed to create a Vec<(String, String))> but not a Vec<(&str, &str)> as expected.

            ...

            ANSWER

            Answered 2018-Mar-04 at 21:21

            Change the graph type to DiGraphMap::, however it does not accept it.

            A GraphMap requires that the node type be copyable. String does not implement Copy.

            Transform a Vec<(String, String)> into a Vec<(&str, &str)>

            As mentioned in the question you linked, this is impossible. What you can do is create a second Vec with &str that reference the original Strings:

            Source https://stackoverflow.com/questions/49087693

            QUESTION

            What is the name of such collection / algorithm that looksup elements via "buckets"
            Asked 2019-Nov-20 at 16:46

            This collection works logically as map but allows to lookup elements by its prefix. It consists of nested Maps in which every nested map corresponds to elements that matches next token of the key.

            For example:

            Lets have bar as a map key. Lets tokenize that bar int "subkeys": b,a,r. Then we would put value using following method (pseudocode)

            1. From root map Map get bor put new Map if absent
            2. From map from previous step get aor put new Map if absent
            3. In map from previous step, set or replace value under key r

            Retrieval is similar (pseudocode)

            1. Take b bucket from root map
            2. Take a bucket from previous bucket
            3. Take r take value under r from previous bucket

            How is such collection called? I would call it a GraphMap or BucketGraph. But what is the proper name?

            ...

            ANSWER

            Answered 2019-Nov-20 at 16:44

            What you describe sounds very much like a Trie, or Prefix Tree. It can be used to sort strings or other objects into buckets based on the individual characters of a word, or words in a sentence, or other types of "sequentian decomposition" (not sure if that is the right term...).

            Source https://stackoverflow.com/questions/58959275

            QUESTION

            Gremlin Java 3.4 withRemote deprecated
            Asked 2019-Aug-16 at 13:43

            So prior to gremlin java 3.4 I used the following code to connect to a remote graph:

            ...

            ANSWER

            Answered 2019-Aug-16 at 13:43

            It's always helpful to review the TinkerPop Upgrade Documentation when you upgrade your graph database dependencies. TinkerPop usually tries to point out deprecation and revised way to do things. In your case, this point here in the upgrade docs is what you need. Specifically, you need to use the new AnonymousTraversalSource rather than EmptyGraph to spawn your GraphTraversalSource:

            Source https://stackoverflow.com/questions/57525502

            QUESTION

            How can I shade inside the curve using JSXgraph
            Asked 2019-Aug-15 at 21:17

            I'm currently trying to shade a quadratic inequality. For that I must be able to shade inside and/or outside of the determined curve. I have looked through JSXgraph documentation and I do not seem to see anything helpful to my problem.

            This answer does not apply to my scenario.

            The current code to create the curve:

            ...

            ANSWER

            Answered 2019-Aug-14 at 08:48

            Indeed, this is not possible out-of-the-box in JSXGraph. But for specific function graphs it should be doable. The trick is to have a further graph which handles the shading.

            For the case of the parabola we clone the points of the parabola to the shading curve and prepend and append further points such that the filled region is always below the curve. Here is the code:

            Source https://stackoverflow.com/questions/57466942

            QUESTION

            How to link LinkedList nodes to map values
            Asked 2019-Jan-11 at 23:33

            I want to implement a graph data structure, where each node is represented by:

            ...

            ANSWER

            Answered 2019-Jan-11 at 23:33

            Things you trying to achieve are not possible the way you do it. It's about addressability and assignability. You should search language specification for this keywoards. Map values aren't addressable, so struct field in that value is not assignable. Also your data structure design looks not very efficient at least for me.

            Seems to me there are no reasons to store values in a map, references would be good enough

            Source https://stackoverflow.com/questions/54154315

            QUESTION

            java enforcing the return type to generic types instead of Object types for constructing map using collectors and streams
            Asked 2018-May-04 at 10:40

            I'm trying to construct Map> from List, List>> pairs. But the problem i'm facing is that it is giving errors saying that Type mismatch: cannot convert from Map to Map>.

            How should i enforce to return Map>

            ...

            ANSWER

            Answered 2018-May-04 at 08:32

            Since your class has Character type (GraphNode) so I think GraphNode::getData also return Character related type.

            But you assigned it to String in Map> so type mismatch occur.

            The resolution is to map the GraphNode::getData to String

            Source https://stackoverflow.com/questions/50170479

            QUESTION

            To assign Country in Country List one by one to Player in PlayerList
            Asked 2017-Oct-07 at 19:19

            I am implementing RISK/Conquer game in JAVA. During the start-up phase of the game, I have to assign countries to each and every player. Just like distributing of cards from deck one by one to each player in the round-robin fashion.

            The relation between Country and Player :

            One Country has One Player (One to One)

            One Player has Many Country (One to Many)

            So far, this is my code:

            Player.java

            ...

            ANSWER

            Answered 2017-Oct-06 at 00:05

            Because you are modifying the collection (playerList) in the same loop, you are getting this ConcurrentModificationException.

            Please go through this SO link. You need to use

            ListIterator

            if you want to add any element in the same loop.

            Source https://stackoverflow.com/questions/46596114

            QUESTION

            malloc error when using std::shared_ptr
            Asked 2017-Feb-28 at 21:34

            I've decided to parallelize a huge program I wrote and eventually I came across the new C++11 smart pointers.

            I had a routine that should be executed many times (usually above 1000 times) that is somewhat expensive. It was ran in a dead simple for loop, what I did was to install this for loop in a method which would be ran by some worker threads.

            Did it so, made some parameters wrapped by a std::shared_ptr, cared for race conditions, everything seemed fine.

            But now, some times, process will be aborted and I am given one of the following errors:

            Process finished with exit code 139 (interrupted by signal 11: SIGSEGV)

            or

            malloc.c:2395: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.

            All of these errors occur while the parallel for is ongoing; not before, not right in the beginning, not in the end, but somewhere in between, which smells me like a race condition not covered.

            The program is huge, but I created a miniature of it that is able to reproduce the problem:

            ...

            ANSWER

            Answered 2017-Feb-28 at 21:34

            Your program has undefined behavior, because you access the object pointed to by kSubgraphs from different threads without mutual exclusion. This happens in this line of code in function foo, which is called from your thread function worker:

            Source https://stackoverflow.com/questions/42518811

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

            Vulnerabilities

            No vulnerabilities reported

            Install graphmap

            To build GraphMap from source type:. You will need a recent GCC/G++ version (>=4.7). Run sudo make install to install the graphmap binary to /usr/bin. More installation instructions can be found in the INSTALL.md file.

            Support

            For additional information, help and bug reports please send an email to one of the following: ivan.sovic@irb.hr, mile.sikic@fer.hr, nagarajann@gis.a-star.edu.sg.
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