Applications/Obitools - Revision history

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2022-11-16T10:53:42Z

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Pysdlb at 13:15, 13 October 2022

2022-10-13T13:15:28Z

Pysdlb at 13:23, 7 June 2018

2018-06-07T13:23:39Z

Pysdlb: Pysdlb moved page Obitools to Applications/Obitools

2017-03-24T11:26:32Z

Pysdlb moved page Obitools to Applications/Obitools

Pysdlb at 11:25, 24 March 2017

2017-03-24T11:25:59Z

Pysdlb at 11:17, 24 March 2017

2017-03-24T11:17:41Z

Pysdlb: Created page with "==Application Details== *Description: The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into accou..."

2017-03-24T11:11:52Z

Created page with "==Application Details== *Description: The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into accou..."

New page

==Application Details==
*Description: The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information
*Version: 1.2.9
*Module: obitools/1.2.9
*Licence: CeCILL 2.1 license

==Usage Areas==

Once installed, the OBITools enrich the Unix command line interface with a set of new commands dedicated to NGS data processing. Most of them have a name starting with the obi prefix. They automatically recognize the input file format amongst most of the standard sequence file formats (i.e. fasta, fastq, EMBL, and GenBank formats). Nevertheless, options are available to enforce some format specificity such as the encoding system used in fastq files for quality codes. Most of the basic Unix commands have their OBITools equivalent (e.g. obihead vs head, obitail vs tail, obigrep vs grep), which is convenient for scientists familiar with Unix. The main difference between any standard Unix command and its OBITools counterpart is that the treatment unit is no longer the text line but the sequence record. As a sequence record is more complex than a single text line, the OBITools programs have many supplementary options compared to their Unix equivalents.

===Metabarcode design and quality assessment===

* ecoPCR: in silico PCR
* ecoPrimers: new barcode markers and primers
* ecotaxstat : getting the coverage of an ecoPCR output compared to the original ecoPCR database
* ecotaxspecificity: Evaluates barcode resolution

===File format conversions===

* obiconvert: converts sequence files to different output formats
* obipr2: converts silva database into an ecoPCR database
* obisilva: converts silva database into an ecoPCR database
* obitaxonomy: manages taxonomic databases
* obitab: converts a sequence file to a tabular file

===Sequence annotations===

* ecotag: assigns sequences to taxa
* obiannotate: adds/edits sequence record annotations
* obiaddtaxids: adds taxids to sequence records using an ecopcr database

===Computations on sequences===

* illuminapairedend: aligns paired-end Illumina reads
* ngsfilter : Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
* obicomplement: reverse-complements sequences
* obiclean: tags a set of sequences for PCR/sequencing errors identification
* obicut: trims sequences
* obijoinpairedend: Joins paired-end reads
* obiuniq: groups and dereplicates sequences

===Sequence sampling and filtering===

* obiextract: extract samples from a dataset
* obigrep: filters sequence file
* obihead: extracts the first sequence records
* obisample: randomly resamples sequence records
* obiselect : selects representative sequence records
* obisplit: Splits a sequence file in a set of subfiles
* obisubset specific options
Options to specify input format
Options to specify output format
Common options
* obisubset modifies sequence attributes
* obisubset used sequence attribute
* obitail: extracts the last sequence records

===Statistics over sequence file===

* ecodbtaxstat: gives taxonomic rank frequency of a given ecopcr database
* obicount: counts the number of sequence records
* obistat: computes basic statistics for attribute values

===Utilities===

* oligotag: Designs a set of oligonucleotides with specified properties
* obidistribute: Distributes sequence records over several sequence records files
* obisort: Sorts sequence records according to the value of a given attribute
* obitaxonomy: manages taxonomic databases
* ecofind: querying a taxonomic database

===Module===

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module obitools/1.2.9
</pre>

==Further Information==

[http://metabarcoding.org/obitools/doc/ http://metabarcoding.org/obitools/doc/]

← Older revision		Revision as of 10:53, 16 November 2022
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	[http://metabarcoding.org/obitools/doc/ http://metabarcoding.org/obitools/doc/]		[http://metabarcoding.org/obitools/doc/ http://metabarcoding.org/obitools/doc/]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

← Older revision		Revision as of 13:15, 13 October 2022
Line 130:		Line 130:

	[http://metabarcoding.org/obitools/doc/ http://metabarcoding.org/obitools/doc/]		[http://metabarcoding.org/obitools/doc/ http://metabarcoding.org/obitools/doc/]
		+
		+	==Navigation==
		+
		+	* [[Main_Page\|Home]]
		+	* [[Applications\|Application support]] *
		+	* [[General\|General]]
		+	* [[Programming\|Programming support]]

@@ Line 101: / Line 101: @@
 #SBATCH --exclusive
-module load obitools/1.2.9
+module add obitools/1.2.9
-module load python/anaconda/4.0/2.7
+module add python/anaconda/4.0/2.7
 export PATH=$PATH:~/applications/ecoPCR/src/

← Older revision	Revision as of 11:26, 24 March 2017
(No difference)

@@ Line 77: / Line 77: @@
 * ecofind: querying a taxonomic database
-[http://metabarcoding.org/obitools/doc/scripts.html http://metabarcoding.org/obitools/doc/scripts.html Obitools]
 ===Module===
@@ Line 84: / Line 86: @@
 [username@login01 ~]$ module obitools/1.2.9
 </pre>

@@ Line 16: / Line 16: @@
 * ecotaxstat : getting the coverage of an ecoPCR output compared to the original ecoPCR database
 * ecotaxspecificity: Evaluates barcode resolution
 ===File format conversions===
@@ Line 24: / Line 25: @@
 * obitaxonomy: manages taxonomic databases
 * obitab: converts a sequence file to a tabular file
 ===Sequence annotations===
@@ Line 30: / Line 32: @@
 * obiannotate: adds/edits sequence record annotations
 * obiaddtaxids: adds taxids to sequence records using an ecopcr database
 ===Computations on sequences===
@@ Line 40: / Line 43: @@
 * obijoinpairedend: Joins paired-end reads
 * obiuniq: groups and dereplicates sequences
 ===Sequence sampling and filtering===
@@ Line 56: / Line 60: @@
 * obisubset used sequence attribute
 * obitail: extracts the last sequence records
 ===Statistics over sequence file===
@@ Line 62: / Line 67: @@
 * obicount: counts the number of sequence records
 * obistat: computes basic statistics for attribute values
 ===Utilities===
@@ Line 71: / Line 77: @@
 * ecofind: querying a taxonomic database
 ===Module===