Online Tools

Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. All exact overlaps between any pair of reads are computed and structured in a graph (overlap step). Basically, the reads are indexed in a prefix array and overlaps are revealed by dichotomic search in the arrays. The graph is then analyzed to remove transitive and spurious edges (layout step). Finally, contigs that can be assembled following unambiguous path in the graph are given as output. Edena allows to produce contigs of several kbp with a near full coverage of the bacterial genome being sequenced.

D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel

2.1.1

Assembler

De novo

Translate Illumina Bustard output to a fastq file

Khalid Belkhir

1

Tool

EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.

Mark Chaisson, Pavel Pevzner, Dumitru Brinza, Haixu Tang, Glenn Tesler

1.1.2

Assembler

De novo

A pipeline to map reads to a reference and call snp with GATK tools.

M. Massaviol & K. Belkhir

1

Mapping - Pipeline

iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Unknown

1

This version processes a de novo assembly to generate a fasta reference file and a gtf file.

iRAP is a flexible computational pipeline for RNA-seq that integrates many existing tools for filtering and mapping reads, quantifying expression and testing for differential expression. It is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line but also provides more advanced users with the ability to customise the options used by their chosen tools.

Unknown

1

Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Unknown

1.1

Tool - Blast

RNA-seq - Apps

Mega BLAST uses a greedy algorithm [1] for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm.

NCBI -Tao Tao

1

Alignment - Blast

Build database giving a sequence file in order to blast query sequences on it using magablast. Treatment performed using formatDB and megablast (8 cores).

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]

1

Blast

This pipeline will assemble paired-end reads with Megahit. The resulting contigs are then mapped on NCBI refseq mitochondrion database to filter mitochondrial sequences.

M. Massaviol & K. Belkhir

1

Alignment - Assembler

PASS has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by Solexa, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming. Pass is useful for single read mapping, paired-end resequensing, small RNA discovery and RNA-seq mapping.

Campagna et al

1.2

Mapping

Test RAD on reference genome

Unknown

1

Mapping

This pipeline implements a RADseq analysis workflow based on the denovo approach of Stacks software.

M. Massaviol & K. Belkhir

1

A reference mapping pipeline using Stacks software.

M. Massaviol & K. Belkhir

1

This interactive application is an R shiny wrapper around the SIMRAD package. Given a particular genome, the user can simulate an inSillico RAD sequencing experiment. Interactively playing with different parameters including fragments size and Restriction enzymes one can assess the amount of sequencing runs needed for a multiplexing design and an expected coverage.

BELKHIR

1

Alignment - Mapping - Tool