Difference between revisions of "Applications/Obitools"

Revision as of 11:26, 24 March 2017

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

Further details are at http://metabarcoding.org/obitools/doc/scripts.html

Module

[username@login01 ~]$ module obitools/1.2.9

Slurm Example


#!/bin/bash

#SBATCH -J obitools_database
#SBATCH -N 1
#SBATCH --ntasks-per-node 40
#SBATCH -o %N.%J.out
#SBATCH -e %N.%J.err 
#SBATCH -p highmem
#SBATCH --exclusive

module load obitools/1.2.9
module load python/anaconda/4.0/2.7
export PATH=$PATH:~/applications/ecoPCR/src/

echo -e "Starttime: $(date)\n"
echo use ecoPCR to simulate an in silico PCR
mkdir 16S_db
echo 16S
ecoPCR -d ./db/embl_last -e 3 -l 50 -L 2000 AGRGTTYGATYMTGGCTCAG GACGGGCGGTGWGTRCA > 16S.v05.ecopcr

echo clean the databse
obigrep -d ./db/embl_last --require-rank=species --require-rank=genus --require-rank=family 16S.v05.ecopcr > 16S_db/16S.v05_clean.fasta

obiuniq -d ./db/embl_last 16S_db/16S.v05_clean.fasta > 16S_db/16S.v05_clean_uniq.fasta

obigrep -d ./db/embl_last --require-rank=family 16S_db/16S.v05_clean_uniq.fasta > 16S_db/16S.v05_clean_uniq_clean.fasta

obiannotate --uniq-id 16S_db/16S.v05_clean_uniq_clean.fasta > 16S_db/db_16S.v05.fasta

echo -e "Endtime: $(date)\n"
echo done

Further Information

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

HPC