lrcaller

https://github.com/decodegenetics/lrcaller

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (7.7%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: DecodeGenetics
License: other
Language: C++
Default Branch: master
Size: 10.1 MB

Statistics

Stars: 16
Watchers: 8
Forks: 4
Open Issues: 3
Releases: 5

Created over 6 years ago · Last pushed over 4 years ago

Metadata Files

Readme Changelog License Citation

LRcaller

Program to estimate genotype structural variants from long read data.

Please see the CHANGELOG before updating from v0.2 to a newer version.

Build instructions

Requirements:

CMake >= 3.4
SeqAn2 (currently the -develop branch is required!)
OpenMP
C++20 capable compiler (tested with GCC≥10 and Clang≥10)

Download or clone this repository with submodules:

sh mkdir -p ~/devel cd ~/devel/ git clone --recurse-submodules https://github.com/DecodeGenetics/LRcaller

And then build it:

sh mkdir -p ~/devel/lrcaller-build/release cd ~/devel/lrcaller-build/release cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-march=native" ../../LRcaller make make test # optional

The -DCMAKE_CXX_FLAGS="-march=native" is not required but highly recommended. Alternatively, you may specify -DCMAKE_CXX_FLAGS="-march=x86-64-v3" to produce a more portable binary (only works on GCC≥10 and Clang≥12).

Usage

lrcaller [OPTIONS] "BAMFILE" "VCF_FILE_IN" "VCF_OUT_FILE"

For details, see lrcaller --help.

Citation

LRcaller is developed at deCODE Genetics by Bjarni V. Halldorsson, Doruk Beyter, Hannes Eggertson (@hannespetur) and Hannes Hauswedell (@h-2). Please cite the following research articel when using LRcaller in any academic work: https://doi.org/10.1038/s41588-021-00865-4

Owner

Name: DecodeGenetics
Login: DecodeGenetics
Kind: organization

Repositories: 8
Profile: https://github.com/DecodeGenetics

Citation (CITATION.cff)

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Halldórsson
    given-names: Bjarni
    orcid: https://orcid.org/0000-0003-0756-0767
  - family-names: Beyter
    given-names: Doruk
    orcid: https://orcid.org/0000-0002-3644-5760
  - family-names: Eggertsson
    given-names: Hannes
    orcid: https://orcid.org/0000-0002-1674-9978
  - family-names: Hauswedell
    given-names: Hannes
    orcid: https://orcid.org/0000-0002-3744-1956
title: "LRcaller"
version: 1.0
doi: 10.1038/s41588-021-00865-4
date-released: 2021-07-28

GitHub Events

Total

Issues event: 3
Issue comment event: 4
Fork event: 1

Last Year

Issues event: 3
Issue comment event: 4
Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 2
Total pull requests: 0
Average time to close issues: 11 days
Average time to close pull requests: N/A
Total issue authors: 2
Total pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: 11 days
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 1.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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