minimap2 | versatile pairwise aligner | Genomics library

by lh3 C Version: v2.26 License: Non-SPDX

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

kandi X-RAY | minimap2 Summary

minimap2 is a C library typically used in Artificial Intelligence, Genomics applications. minimap2 has no bugs, it has no vulnerabilities and it has medium support. However minimap2 has a Non-SPDX License. You can download it from GitHub, GitLab.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Support

Quality

Security

License

Reuse

Support

minimap2 has a medium active ecosystem.

It has 1468 star(s) with 372 fork(s). There are 80 watchers for this library.

It had no major release in the last 12 months.

There are 125 open issues and 836 have been closed. On average issues are closed in 8 days. There are 7 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of minimap2 is v2.26

Quality

minimap2 has no bugs reported.

Security

minimap2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

minimap2 has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

minimap2 releases are available to install and integrate.

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

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of minimap2

Get all kandi verified functions for this library.

minimap2 Key Features

No Key Features are available at this moment for minimap2.

minimap2 Examples and Code Snippets

Julia - AttributeError("'PyCall.jlwrap' object has no attribute 'encode'")

Python

Lines of Code : 7

License : Strong Copyleft (CC BY-SA 4.0)

Copy

for record in FASTQ.Reader(GzipDecompressorStream(open("data_file.fastq.gz")))
    seq = string(sequence(record))
    check = py"mappy"(seq,aligner)
    
end
close(reader)

Community Discussions

Trending Discussions on minimap2

Multiple outputs to single list input - merging BAM files in Nextflow

Snakemake: MissingInputException with inconsistent naming scheme

Snakemake problem: Merge all files together with space delimiter instead of iterating through it

QUESTION

Multiple outputs to single list input - merging BAM files in Nextflow

Asked 2021-Mar-04 at 15:53

I am attempting to merge x number of bam files produced via performing multiple alignments at once (on batches of y number of fastq files) into one single bam file in Nextflow.

So far I have the following when performing the alignment and sorting/indexing the resulting bam file:

...

ANSWER

Answered 2021-Mar-04 at 15:53

The simplest fix would probably to stop passing the static dirstring and runstring around via channels:

Source https://stackoverflow.com/questions/66475893

QUESTION

Snakemake: MissingInputException with inconsistent naming scheme

Asked 2020-Sep-10 at 15:23

I am trying to process MinION cDNA amplicons using Porechop with Minimap2 and I am getting this error.

...

ANSWER

Answered 2020-Sep-09 at 22:50

First of all, you can always debug the problems like that specifying the flag --printshellcmds. That would print all shell commands that Snakemake runs under the hood; you may try to run them manually and locate the problem.

As for why your rule doesn't produce any output, my guess is that samtools requires explicit filenames or - to use stdin:

Samtools is designed to work on a stream. It regards an input file '-' as the standard input (stdin) and an output file '-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error output (stderr).

So try that:

Source https://stackoverflow.com/questions/63818429

QUESTION

Snakemake problem: Merge all files together with space delimiter instead of iterating through it

Asked 2020-May-05 at 10:01

I was trying to run a command which ideally looks like this,

minimap2 -a -x map-ont -t 20 /staging/reference.fasta fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample01.bam

Similarly, I have multiple samples (referring to fastq/sample01.fastq) in the folder.

The snakemake file I wrote to automate this behaviour is, however, parsing all files at once in the command like,

minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam

I have pasted the code and logs below. Please help me try to figure out this mistake.

Code

...

ANSWER

Answered 2020-May-05 at 10:01

The expand function is used to create a list. Thus, in your rule minimap, you're telling snakemake that you want all fastq files as input and that the rule will produce as many bam files. What you want is a rule that will be triggered for every sample using a wildcard:

Source https://stackoverflow.com/questions/61608615

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

Vulnerabilities

No vulnerabilities reported

Install minimap2

You can download it from GitHub, GitLab.

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 .

Find more information at: