V-FAT 1.1 – Automated Finishing, Annotation, and QA tool for Viral Assemblies

V-FAT 1.1

:: DESCRIPTION

V-FAT (Viral Finishing and Annotation Toolkit) is a tool to perform automated computational finishing and annotation of de novo viral assemblies. V-FAT uses reference and read data to order and merge contigs, correct frameshifts, and produce NCBI-ready annotation files. It also performs a set of quality assurance measurements including coverage computation by gene or amplicon and identification of potential consensus errors.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

V-FAT

:: MORE INFORMATION

Citation

Charlebois, P, Yang, X, Newman, RM, Henn, MR, Zody, MC (2012)
V-FAT: a post-assembly pipeline for the finishing and annotation of viral genomes.
Submitted.

VICUNA 1.1 – de novo Assembler for Ultra-deep Sequence data

VICUNA 1.1

:: DESCRIPTION

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VICUNA

:: MORE INFORMATION

Citation

Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J. Lennon, Joshua Z. Levin, James Qu, Elizabeth M. Ryan, Michael C. Zody, and Matthew R. Henn (2012)
De novo assembly of highly diverse viral populations.
BMC Genomics 13:475.

RC454 1.2 – Read Alignment and Error Correction tool for Cleaning 454 Reads of Process Errors

RC454 1.2

:: DESCRIPTION

RC454 (ReadClean454) is a program that takes a set of 454 read and quality files as well as a consensus assembly for those reads and corrects for known 454 error modes such as homopolymer indels and carry forward/incomplete extension (CAFIE).It will also correct for any indel that breaks the reading frame, unless it occurs in more than 25% of the reads.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RC454

:: MORE INFORMATION

AV454 1.0 – de novo Consensus Assembler designed for reads derived from diverse Viral Populations

AV454 1.0

:: DESCRIPTION

AV454 (AssembleViral454) is an assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AV454

:: MORE INFORMATION

SCUBAT – Scaffolding Contigs using BLAT and Transcripts

SCUBAT

:: DESCRIPTION

SCUBAT is a perl script uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
BLAT
CAP3
Perl

:: DOWNLOAD

SCUBAT

:: MORE INFORMATION

QSRA 1.0 – Quality-value guided de novo Short Read Assembler

QSRA 1.0

:: DESCRIPTION

QSRA (Quality-value-guided Short Read Assembler) is a quality-value guided de novo short read assembler. QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

QSRA

:: MORE INFORMATION

Citation

Bryant DW, Wong WK, Mockler TC.
QSRA – a quality-value guided de novo short read assembler.
BMC Bioinformatics 2009, 10:69

GenSeed 1.0.22 – Seed-driven progressive Assembly program

GenSeed 1.0.22

:: DESCRIPTION

GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence.

::DEVELOPER

GenSeed Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

GenSeed

:: MORE INFORMATION

Citation:

Sobreira, T.J.P. & Gruber, A. (2008).
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
Bioinformatics, doi: 10.1093/bioinformatics/btn283

GAM – Genome Assemblies Merger

GAM

:: DESCRIPTION

GAM is a free parallel software tool to integrate two different assemblies and improves the overall quality of the genome sequences by merging them. It discovers and align similar sequences by using the positions of placed reads. An order sequence of reads contiguous on the same contig is called frame. When the same frame is shared by both original assemblies, GAM dubs it block.

::DEVELOPER

Istituto di Genomica Applicata and at University of Udine.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GAM

:: MORE INFORMATION

Citation

A. Casagrande, C. Del Fabbro, S. Scalabrin, A. Policriti.
GAM: Genomic Assemblies Merger. A Graph Based Method to Integrate Different Assemblies
Proceedings of the Third IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2009), Washington D.C. (USA), November 1-4 2009.

SEQuel 1.0.2 – Improving the Accuracy of Genome Assemblies

SEQuel 1.0.2

:: DESCRIPTION

SEQuel is a tool for improving the accuracy of high throughput sequencing assemblies.

::DEVELOPER

Roy Ronen and Christina Boucher in Pavel Pevzner’s lab at the University of California, San Diego.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Perl

:: DOWNLOAD

SEQuel

:: MORE INFORMATION

Citation

R. Ronen, C. Boucher, H. Chitsaz, and P. Pevzner.
SEQuel: Improving the Accuracy of Genome Assemblies.
Bioinformatics (2012) 28 (12): i188-i196.

BioLign 4.0.6 – Assembly Editor

BioLign 4.0.6

:: DESCRIPTION

BioLign is a multiple contig alignment editor which constructs multiple alignments from the output generated by the PHRAP contig program (Phil Green, U. of Washington), and allows integrated and synchronized viewing and unrestricted editing of both the base calls of the contig and the alignment itself. Raw trace data is maintained and manual alignment adjustments as well as manual character insertions and deletions are synchronized automatically with the raw data. Sequence traces may visually inspected and edited in a synchronized interface which opens and closes traces automatically as you pass through them in the contig, and lines up all relevant traces at a user-defined point to the same point in the contig. A user-defined coloring scheme allows up to ten levels of coloring within the alignment window and the trace data view to reflect Phrap-assigned sequence quality. Traces graphically display Phred-assigned quality for each individual trace. BioLign was built upon the BioEdit interface (by the same author), and includes the entire BioEdit freeware package integrated with it. The alignment interface of a BioLign contig alignment is very similar to a BioEdit alignment document.

::DEVELOPER

Tom Hall (THall@isisph.com)

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

BioLign

:: MORE INFORMATION