LRSIM | 10x Genomics Reads Simulator | Genomics library

by aquaskyline C Version: 1.0 License: MIT

X-Ray Key Features Code Snippets(3)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | LRSIM Summary

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

This package simulates whole genome sequencing using 10X Genomics Linked Read technology. We have attempted to realistically capture all of the relevant steps of the 10X protocol so that it can be used to faithfully evaluate linked read sequencing of different genomes, mutation rates, input libraries, and short read sequencing conditions in silico. We have tested the package with LongRanger, SuperNova, HapCUT2, fragScaff and ARCS to confirm that variant identifation, phasing, de novo assembly and scaffolding are supported. We also encourage users to use these simulations to aid in the development of novel algorithms. Please feel free to contact us if your pipelines require additional features.

Support

Quality

Security

License

Reuse

Support

LRSIM has a low active ecosystem.

It has 47 star(s) with 13 fork(s). There are 6 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 33 have been closed. On average issues are closed in 56 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of LRSIM is 1.0

Quality

LRSIM has 0 bugs and 0 code smells.

Security

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

LRSIM code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

LRSIM 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

LRSIM releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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LRSIM Key Features

No Key Features are available at this moment for LRSIM.

LRSIM Examples and Code Snippets

Parameters

Lines of Code : 41

License : Permissive (MIT)

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    Usage:   ./simulateLinkedReads.pl -r/-g  -p  [options]

    Reference genome and variants:
    -d INT      Haplotypes to simulate [2]
    -g STRING   Haploid FASTAs separated by comma. Overrides -r and -d.
    -1 INT      1 SNP per INT base pairs

License

Lines of Code : 19

License : Permissive (MIT)

Copy

  The MIT License (MIT)
  Copyright (c) 2016 Ruibang Luo 
 
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restr

Getting Started

Lines of Code : 5

License : Permissive (MIT)

Copy

git clone --recursive https://github.com/aquaskyline/LRSIM.git
cd LRSIM
sh make.sh
cd test
sh test.sh

Community Discussions

Trending Discussions on LRSIM

Perl can't locate inline C module: "Had problems bootstrapping Inline module"

QUESTION

Perl can't locate inline C module: "Had problems bootstrapping Inline module"

Asked 2019-Jun-21 at 12:21

Getting the error at the below when trying to run a Perl script. The script is from this package: https://github.com/aquaskyline/LRSIM

...

ANSWER

Answered 2019-Jun-21 at 12:21

Around line 24093 of your strace log make says something about Clock skew detected. Maybe the issue is related to the file system the script is running on (/mnt/fargen/experiments/...)?

make relies on accurate time stamps to determine which files need to be updated and to schedule its actions. If the time stamps are wrong, files might be built incorrectly or not at all.

The reason make is involved at all is because behind the scenes Inline::C extracts the embedded C code and creates an ad-hoc Perl module for it, including an XS file, Makefile.PL, and the whole machinery. Then it invokes perl Makefile.PL && make && make install, which is supposed to create a .so file and copy it in a location where perl can load it (this .so file is the loadable object mentioned in the error message).

Source https://stackoverflow.com/questions/56701591

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

Vulnerabilities

No vulnerabilities reported

Install LRSIM

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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