ngmlr | read mapper designed to align PacBio | Genomics library

by philres C++ Version: v0.2.7 License: MIT

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kandi X-RAY | ngmlr Summary

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

CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions). With 10 cores (AMD Opteron 6348), ngmlr currently takes about 90 minutes and 10 GB RAM for aligning 3Gbp (~ 1x human data) of Pacbio reads.

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Support

ngmlr has a low active ecosystem.

It has 222 star(s) with 34 fork(s). There are 20 watchers for this library.

It had no major release in the last 12 months.

There are 36 open issues and 52 have been closed. On average issues are closed in 44 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ngmlr is v0.2.7

Quality

ngmlr has 0 bugs and 0 code smells.

Security

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

ngmlr code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ngmlr 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

ngmlr releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 355 lines of code, 19 functions and 2 files.

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

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ngmlr Key Features

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ngmlr Examples and Code Snippets

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Community Discussions

Trending Discussions on ngmlr

name input/output files in snakemake according to variable (not wildcard) in config.yaml

Can CMake require static libraries (e.g., ZLIB)?

QUESTION

name input/output files in snakemake according to variable (not wildcard) in config.yaml

Asked 2019-Oct-24 at 14:48

I am trying to edit and run a snakemake pipeline. In a nutshell, the snakemake pipeline calls a default genome aligner (minimap) and produces output files with this name. I am trying to add a variable aligner to config.yaml to specify the aligner I want to call. Also (where I am actually stuck), the output files should have the name of the aligner specified in config.yaml.

My config.yaml looks like this:

...

ANSWER

Answered 2019-Oct-24 at 14:48

You are close!

The way wildcards work in snakemake is they get interpreted 'last', while f-strings get interpreted first. To not interpret a curly brace in an f-string you can escape it with another curly brace, like so:

Source https://stackoverflow.com/questions/58540231

QUESTION

Can CMake require static libraries (e.g., ZLIB)?

Asked 2017-Jun-24 at 16:51

It has been years since I worked in C++, and I've never used CMake before. I'm trying to compile a program called ngmlr, which uses CMake. It worked seamlessly on other systems I tried to build it on. This time around, CMake finds ZLIB (Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")), as required by ngmlr, but the subsequent make fails with ld: cannot find -lz.

I think I know what's happening: CMake found the dynamic ZLIB library (libz.so), but the CMakeLists.txt file requires static (I found the following option in the file: option(STATIC "Build static binary" ON)). As far as I can tell, the static library (libz.a) is missing on this machine. It's not in the same /usr/lib64 directory as libz.so. locate is not available.

Questions:

Does that seem correct?
For education, assuming this is the problem, can you force CMake to look specifically for static ZLIB? e.g., since the developer required static, it would have been nice to immediately know the missing static library was the problem, rather than the embarrassingly long amount of time it took me to figure it out.

I've looked extensively for a clear answer to both, but didn't find anything conclusive (e.g., Force cmake to use static libraries).

UPDATE I did confirm that the problem is that ld could not find the static library. Now I'm particularly interested to know if the developer can tell CMake to throw an error if the static libraries are not present, and save someone else.

cmake version 2.8.8

...

ANSWER

Answered 2017-Jun-24 at 03:11

Your CMakeLists.txt probably has this somewhere:

Source https://stackoverflow.com/questions/44731248

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Vulnerabilities

No vulnerabilities reported

Install ngmlr

Download binary from github and unzip or or pull docker . For updates follow.

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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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