kourami | Kourami : Graph-guided assembly for HLA alleles | Genomics library

 by   Kingsford-Group Java Version: v0.9.6 License: BSD-3-Clause

kandi X-RAY | kourami Summary

kandi X-RAY | kourami Summary

kourami is a Java library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. kourami has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Kourami is a graph-guided assembler for HLA haplotypes covering typing exons (exons 2 and 3 for Class I and exon 3 for Class II) using high-coverage whole genome sequencing data. Kourami constructs highly accurate haplotype sequences at 1-bp resolution by first encoding currently available HLA allelic sequences from IPD-IMGT/HLA Database ( ) as partial-ordered graphs. Each database allele is naturally encoded as a path through the graph and any detectable genetic variations (SNPs or indels) not captured by the known sequences are added to the graph by graph-modification based on read alignment to capture differences novel alleles have compared to known sequences. Unlike previously available WGS-based HLA typing methods (database-matching techniques), Kourami direclty assembles both haplotypes for each HLA gene (HLA-A, -B, -C, -DQA1, -DQB1, -DRB1). From version 0.9.4 or later, Kourami supports additional HLA loci. It also provides the typing result (6-digit 'G' resolution) by outputing the best matching alleles among the known sequences whenever 'G' grouping information is available.

            kandi-support Support

              kourami has a low active ecosystem.
              It has 29 star(s) with 10 fork(s). There are 17 watchers for this library.
              It had no major release in the last 12 months.
              There are 10 open issues and 20 have been closed. On average issues are closed in 22 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of kourami is v0.9.6

            kandi-Quality Quality

              kourami has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              kourami is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              kourami releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed kourami and discovered the below as its top functions. This is intended to give you an instant insight into kourami implemented functionality, and help decide if they suit your requirements.
            • Remove unsupported paths
            • Calculate the maximum likelihood of two paths
            • Obtains the path probabilities for each edge in the given graph
            • Calculate the phred score for a single allele
            • Print the intersection score of two sequences
            • Print interbble results
            • Print the results of the possible sequences
            • Runs KVLami
            • Gather all paths found in the superBubble
            • Calculates the hydrogenages between two superbbles
            • Processes a block and computes its bases
            • Print to standard out
            • Checks to see if it is phased with another path
            • Get the number of active paths
            • Generate sequence from base boundaries
            • Gets the union after the intersection of the given edge
            • Traverses and returns true if necessary
            • Loads the graph and builds HLA graphs
            • Compare the interbubble
            • Calculate the likelihood score for a single allele
            • Demonstrates how to read the IMGT file
            • Inserts columns by insertion size
            • Load the alignment format from the IMGT file
            • Removes non unique edge only
            • Decompose all ST paths in the bubble
            • Build the graph
            Get all kandi verified functions for this library.

            kourami Key Features

            No Key Features are available at this moment for kourami.

            kourami Examples and Code Snippets

            No Code Snippets are available at this moment for kourami.

            Community Discussions


            search for regex match between two files using python
            Asked 2022-Apr-09 at 00:49

            I´m working with two text files that look like this: File 1



            Answered 2022-Apr-09 at 00:49

            Perhaps you are after this?

            Source https://stackoverflow.com/questions/71789818


            Is there a way to permute inside using to variables in bash?
            Asked 2021-Dec-09 at 23:50

            I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

            This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

            The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

            1. Input files: Highland.ped - Midland.ped - Lowland.ped
            2. Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
            3. Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

            The general code is:



            Answered 2021-Dec-09 at 23:50

            Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

            Source https://stackoverflow.com/questions/70298074


            BigQuery Regex to extract string between two substrings
            Asked 2021-Dec-09 at 01:11

            From this example string:



            Answered 2021-Dec-09 at 01:11

            use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

            if applied to sample data in your question - output is

            Source https://stackoverflow.com/questions/70283253


            how to stop letter repeating itself python
            Asked 2021-Nov-25 at 18:33

            I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it



            Answered 2021-Nov-25 at 18:33

            As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

            Source https://stackoverflow.com/questions/70112201


            Split multiallelic to biallelic in vcf by plink 1.9 and its variant name
            Asked 2021-Nov-17 at 13:56

            I am trying to use plink1.9 to split multiallelic into biallelic. The input is that



            Answered 2021-Nov-17 at 09:45


            Delete specific letter in a FASTA sequence
            Asked 2021-Oct-12 at 21:00

            I have a FASTA file that has about 300000 sequences but some of the sequences are like these



            Answered 2021-Oct-12 at 20:28

            You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

            For example:

            Source https://stackoverflow.com/questions/69545912


            How to get the words within the first single quote in r using regex?
            Asked 2021-Oct-04 at 22:27

            For example, I have two strings:



            Answered 2021-Oct-04 at 22:27

            For your example your pattern would be:

            Source https://stackoverflow.com/questions/69442717


            Does Apache Spark 3 support GPU usage for Spark RDDs?
            Asked 2021-Sep-23 at 05:53

            I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

            I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

            On querying in Hail forum, I got the response that

            That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

            So, does Spark3 not support GPU usage for RDD interfaces?



            Answered 2021-Sep-23 at 05:53

            As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

            Source: Link

            Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

            Here, an answer from spark-rapids team

            Source: Link

            We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

            Source https://stackoverflow.com/questions/69273205


            Aggregating and summing columns across 1500 files by matching IDs in R (or bash)
            Asked 2021-Sep-07 at 13:09

            I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:



            Answered 2021-Sep-07 at 11:10


            Usage of compression IO functions in apache arrow
            Asked 2021-Jun-02 at 18:58

            I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.



            Answered 2021-Jun-02 at 18:58

            Here is an example program that inflates a compressed zlib file and reads it as CSV.

            Source https://stackoverflow.com/questions/67799265

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


            No vulnerabilities reported

            Install kourami

            To install Kourami, you must have following installed on your system:.
            JDK 1.8+
            Apache Maven (3.3+) or Apache Ant (1.9+) is required (we recommend Maven for easy dependency downloads) OR you must have dependencies downloaded and added to your CLASSPATH. Then you can compile using javac. To use Ant, you must have dependencies downloaded and place jars under 'exjars' directory. 'exjars' directory must be created.


            Kourami is, and will continue to be, freely and actively supported on a best-effort basis. If you need industrial-grade technical support, please consider the options at oceangenomics.com/support.
            Find more information at:

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