DNAscan | efficient bioinformatics pipeline | Genomics library

by KHP-Informatics HTML Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | DNAscan Summary

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

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage. DNAscan can analyse 40x whole genome NGS data in ~8 hours, using as little as 8 cpus and 16 Gbs of RAM while guaranteeing a very high performance. We do this by exploiting state-of-the-art bioinformatics tools. DNAscan can screen your DNA NGS data for single nucleotide variants, small indels, structural variants, repeat expansions, viral (or any other organism’s) genetic material. Its results are annotated using a wide range of databases including ClinVar, EXAC, dbSNP and CADD and uploaded onto the gene.iobio platform for an on-the-fly analysis/interpretation. Figure 1. Central panel: Pipeline overview. DNAscan accepts sequencing data, and optionally variant files. The pipeline firstly performs an alignment step (details in the left panel), followed by a customizable data analysis protocol (details in the right panel). Finally, results are annotated and a user friendly report is generated. Right panel: detailed description of the post alignment analysis pipeline (intensive mode). Aligned reads are used by the variant calling pipeline (Freebayes + GATK HC + Bcftools), both aligned and unaligned reads are used by Manta and ExpensionHunter (for which known repeat description files have to be provided) to look for structural variants. The unaligned reads are mapped to a database of known viral genomes (NCBI database) to screen for the presence of their genetic material in the input sequencing data. Left panel: Alignment stage description. Raw reads are aligned with HISAT2. Resulting soft/hard-clipped reads and unaligned reads are realigned with BWA mem and then merged with the others using samtools.

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Support

DNAscan has a low active ecosystem.

It has 35 star(s) with 20 fork(s). There are 12 watchers for this library.

It had no major release in the last 6 months.

There are 2 open issues and 1 have been closed. On average issues are closed in 243 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of DNAscan is current.

Quality

DNAscan has 0 bugs and 0 code smells.

Security

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

DNAscan code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

DNAscan is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

DNAscan releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

It has 8095 lines of code, 0 functions and 8 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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DNAscan Key Features

No Key Features are available at this moment for DNAscan.

DNAscan Examples and Code Snippets

No Code Snippets are available at this moment for DNAscan.

Community Discussions

Trending Discussions on Genomics

search for regex match between two files using python

Is there a way to permute inside using to variables in bash?

BigQuery Regex to extract string between two substrings

how to stop letter repeating itself python

Split multiallelic to biallelic in vcf by plink 1.9 and its variant name

Delete specific letter in a FASTA sequence

How to get the words within the first single quote in r using regex?

Does Apache Spark 3 support GPU usage for Spark RDDs?

Aggregating and summing columns across 1500 files by matching IDs in R (or bash)

Usage of compression IO functions in apache arrow

QUESTION

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

...

ANSWER

Answered 2022-Apr-09 at 00:49

Perhaps you are after this?

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

QUESTION

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.

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

The general code is:

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ANSWER

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

QUESTION

BigQuery Regex to extract string between two substrings

Asked 2021-Dec-09 at 01:11

From this example string:

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ANSWER

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

QUESTION

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

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ANSWER

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

QUESTION

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

...

ANSWER

Answered 2021-Nov-17 at 09:45

I used bcftools to complete the task.

https://github.com/samtools/bcftools/issues/1193

Source https://stackoverflow.com/questions/70001737

QUESTION

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

...

ANSWER

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

QUESTION

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:

...

ANSWER

Answered 2021-Oct-04 at 22:27

For your example your pattern would be:

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

QUESTION

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?

...

ANSWER

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

QUESTION

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:

...

ANSWER

Answered 2021-Sep-07 at 11:10

a tidyverse solution

Source https://stackoverflow.com/questions/69086946

QUESTION

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.

...

ANSWER

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

Vulnerabilities

No vulnerabilities reported

Install DNAscan

DNAscan can be used with the following human genome reference builds: hg19, hg38, grch37, grch38. The used build can be specified when running DNAscan by using the option -reference (options are hg19, hg38, grch37 and grch38). However, DNAscan uses Annovar to annotate the variants and Annovar is only compatible with hg19 and hg38 at present. Therefore, if the user wants to use grch37 and grch38 the pipeline will skip the annotation step. We are currently working on this and it will be possible to run DNAscan on grch37 and grch38 without limitations.
Copy and paste the following commands in your command line to download the whole NCBI database of complete viral genomes. Copy and paste the following commands in your command line to download the whole NCBI database of complete bacterial genomes (this might take a long time). Copy and paste the following commands in your command line to download the whole NCBI database of complete fungi genomes.

Support

Here’s how we suggest you go about proposing a change to this project:. Using the web-based interface to make changes is fine too, and will help you by automatically forking the project and prompting to send a pull request too.

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