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NGLess: NGS Processing with Less Work — ngless 0.0 documentation

Taxonomic profiling using mOTUs with ngless. NGLess: NGS Processing with Less Work. NGLess: NGS Processing with Less Work. NGLess is a domain-specific language for NGS (next-generation sequencing data) processing. Software, currently available as a preview only. Please get in touch. If you want to use it in your work.For questions, you can also use the ngless mailing list. NGLess is best illustrated by an example:. Converting a SAM file to a FASTQ file. Getting aligned reads from a SAM file as FASTQ file.

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Taxonomic profiling using mOTUs with ngless. NGLess: NGS Processing with Less Work. NGLess: NGS Processing with Less Work. NGLess is a domain-specific language for NGS (next-generation sequencing data) processing. Software, currently available as a preview only. Please get in touch. If you want to use it in your work.For questions, you can also use the ngless mailing list. NGLess is best illustrated by an example:. Converting a SAM file to a FASTQ file. Getting aligned reads from a SAM file as FASTQ file.

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NGLess: NGS Processing with Less Work — ngless 0.0 documentation | ngless.readthedocs.io Reviews

https://ngless.readthedocs.io

Taxonomic profiling using mOTUs with ngless. NGLess: NGS Processing with Less Work. NGLess: NGS Processing with Less Work. NGLess is a domain-specific language for NGS (next-generation sequencing data) processing. Software, currently available as a preview only. Please get in touch. If you want to use it in your work.For questions, you can also use the ngless mailing list. NGLess is best illustrated by an example:. Converting a SAM file to a FASTQ file. Getting aligned reads from a SAM file as FASTQ file.

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Taxonomic profiling using mOTUs with ngless — ngless 0.0 documentation

http://ngless.readthedocs.io/en/latest/motus.html

Taxonomic profiling using mOTUs with ngless. Taxonomic profiling using mOTUs with ngless. Taxonomic profiling using mOTUs with ngless. You can use ngless to compute mOTU profiles. This requires the use of the (standard) motus module:. This module (with the motus database) will be downloaded the first time you use it. You can use all the ngless functionality to load and preprocess. Producing the motus tables is done in three steps. Map the samples against the. Module, everything else is standard ngless.

2

Available Reference Genomes — ngless 0.0 documentation

http://ngless.readthedocs.io/en/latest/Organisms.html

Taxonomic profiling using mOTUs with ngless. NGLess provides builtin support for the most widely used model organisms (human, mouse, yeast, C. elegans, . see the full table below). This makes it easier to use the tool when using these organisms as some knowledge is already built in. NGLess provides archives containing data sets of organisms. Is also provided gene annotations that provide information about protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

3

Tutorial — ngless 0.0 documentation

http://ngless.readthedocs.io/en/latest/tutorial.html

Taxonomic profiling using mOTUs with ngless. This example will use data from a real experiment stored at EMBL-EBI. The data can be accessed at http:/ www.ebi.ac.uk/ena/data/view/SRP023199. And represent HeLa cells. The idea is to preprocess the data set, map it against the human genome and count the reads that overlap with known genes. We will use the fastQ file ftp:/ ftp.sra.ebi.ac.uk/vol1/fastq/SRR867/SRR867735/SRR867735.fastq.gz. That can be accessed in the table, on column Sample accession. Syntax is...

4

Configuration — ngless 0.0 documentation

http://ngless.readthedocs.io/en/latest/configuration.html

Taxonomic profiling using mOTUs with ngless. Ngless’ results do not change because of configuration or command line options. The ngless script always has complete information on what is computed. What configuration options change are details of how the results are computed such as where to store intermediate files and how many CPU cores to use. Ngless gets its configuration options from the following sources:. A global configuration file. A user configuration file (typically. Number of CPUs to use.

5

Standard library — ngless 0.0 documentation

http://ngless.readthedocs.io/en/latest/stdlib.html

Full “parallel” example. Taxonomic profiling using mOTUs with ngless. The standard library in ngless are a set of modules which are built in to the language. This module allows you to run several parallel computations. It provides two functions:. Takes a list of strings and returns a single element. It uses the filesystem to obtain a lock file so that if multiple processes are running at once, each one will return a different element. Ngless also marks results as. Once you have run a script to completion.

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NGLess: NGS Processing with Less Work — ngless 0.0 documentation

Taxonomic profiling using mOTUs with ngless. NGLess: NGS Processing with Less Work. NGLess: NGS Processing with Less Work. NGLess is a domain-specific language for NGS (next-generation sequencing data) processing. Software, currently available as a preview only. Please get in touch. If you want to use it in your work.For questions, you can also use the ngless mailing list. NGLess is best illustrated by an example:. Converting a SAM file to a FASTQ file. Getting aligned reads from a SAM file as FASTQ file.

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