sortmerna | generation sequence filtering and alignment tool | Genomics library

by biocore C++ Version: v4.3.6 License: GPL-3.0

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

kandi X-RAY | sortmerna Summary

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

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

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sortmerna has a low active ecosystem.

It has 162 star(s) with 58 fork(s). There are 17 watchers for this library.

It had no major release in the last 12 months.

There are 38 open issues and 221 have been closed. On average issues are closed in 211 days. There are 6 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of sortmerna is v4.3.6

Quality

sortmerna has 0 bugs and 0 code smells.

Security

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

sortmerna code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

sortmerna is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

sortmerna releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 1251 lines of code, 35 functions and 3 files.

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

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sortmerna Key Features

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sortmerna Examples and Code Snippets

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Community Discussions

Trending Discussions on sortmerna

snakemake job submission in sequential manner

Snakemake Wildcards SyntaxError

execute snakemake rule as last rule

QUESTION

snakemake job submission in sequential manner

Asked 2020-Sep-14 at 09:08

I wrote a snakemake pipeline for performing sortmeRNA version 4.2.0. The pipeline is as follows, and works perfectly when I run it for 1 sample:

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ANSWER

Answered 2020-Sep-14 at 09:08

The problem here is that {SAMPLES} in your inputs and outputs is a wildcard. In the shell it is read as the global variable defined above the rule.

You should use {wildcards.SAMPLES} in the shell section:

Source https://stackoverflow.com/questions/63872864

QUESTION

Snakemake Wildcards SyntaxError

Asked 2020-Jan-21 at 16:26

I know this is a common error and I already checked other posts but it didn't resolved my issue. I would like to use the name of the database I use for SortMeRNA rule (rRNAdb=config["rRNA_database"]) the same way I use version=config["genome_version"]. But obviously, I can't.

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ANSWER

Answered 2020-Jan-21 at 16:26

All output files need to have same wildcards, or else it would cause conflict in resolving job dependencies. Not all files in output: have {rRNAdb} wildcard, which is causing this problem. For example, if you have two {rRNAdb} values, both would write to file "{OUTDIR}/temp/{sample}.fastq", which snakemake correctly doesn't allow.

Source https://stackoverflow.com/questions/59824038

QUESTION

execute snakemake rule as last rule

Asked 2020-Jan-16 at 13:46

I tried to create a snakemake file to run sortmeRNA pipeline:

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ANSWER

Answered 2020-Jan-16 at 13:46

For Snakemake to connect the input of one rule to the output of another, they will need to be identical. The way you describe the output of sortmeRNA and the input unmerge_paired do not work together, whether you put temp() around it or not.

Source https://stackoverflow.com/questions/59766049

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