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ABySS

Assembler

 

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. We propose MPI version using 4 cores on the platform.

Author(s)

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ


Version

1.2.1


Subsections

Assembler


Tags

parallel - De novo


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After read cleaning this pipeline will call Abyss for denovo assembly in contigs. The resulting contigs can be further assembled with CAP3. The contigs are then blasted against a provided multi-fasta file and/or ncbi databases. If a blastx on nr is chosen the result can be used to annotate the best hits with blast2go.

Author(s)

MBB dev


Version

1


Subsections

Pipeline - Blast - Assembler


Tags

De novo


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Author(s)

Khalid


Version

1


Subsections

Pipeline - Assembler


Tags

De novo


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Bl2seq

Blast

 

The program bl2seq is designed to compare two input FASTA sequences directly bypassing the formatdb step. This allows users to quickly assess the similarities between two input sequences. The program is capable of performing six types of blast searches: blastn, blastp, blastx, tblastn, tblastx, and megabalst in place of blastn.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

1


Subsections

Blast


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Used in order to build a database on a given sequence file and perform a Blast on it. Useful to realize reciprocal Blast. The proposed version of formatDB and Blast are those including MPI compatibility. Then each execution use 8 cores to reduce execution time.

Author(s)

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


Version

1


Subsections

Blast


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BLAST2

Blast

 

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

2


Subsections

Blast


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Perform blast X on Nucleotidic sequences in order to extract GO terms associated. Use blast2 with blastX program to retrieve XML formated results then launch b2g4pipe using Gene Ontology (assocdb-data 2010-12).

Optionally accepts XML blast result to avoid the blastX on NCBI NR database step.

Author(s)

MBB development team


Version

2


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BLASTClust is a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. The program begins with pairwise matches and places a sequence in a cluster if the sequence matches at least one sequence already in the cluster. In the case of proteins, the blastp algorithm is used to compute the pairwise matches; in the case of nucleotide sequences, the Megablast algorithm is used.

Author(s)

Ilya Dondoshansky, Yuri Wolf


Version

2.2.21


Subsections

Blast


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Bowtie

Mapping

 

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Author(s)

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast


Version

0.12.5


Subsections

Mapping


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BWA Sampe

Mapping

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Mapping - Assembler


Tags

bwa


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BWA Samse

Assembler

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Assembler - Mapping


Tags

bwa


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CAP3

Assembler

 

The program has a capability to clip 5′ and 3′ low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors and link contigs.

Author(s)

Huang, X. and Madan, A.


Version

1


Subsections

Assembler


Tags

under development


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Pipeline for de Novo assembly of reads from a mix of 454 and Illumina sequencing technologies.

Author(s)

Vincent Cahais


Version

1


Tags

under development


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Cufflinks

Expression

 

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

Author(s)

Cole Trapnell et al.


Version

0.9.2


Subsections

Expression


Tags

RNA-seq


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Edena

Assembler

 

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.

Author(s)

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


Version

2.1.1


Subsections

Assembler


Tags

De novo


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