:: DESCRIPTION
CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CLASS is a software tool for accurately assembling splice variants using local read coverage patterns of RNA-seq reads, contiguity constraints from read pairs and spliced reads, and optionally information about gene structure extracted from cDNA sequence databases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.
CLASS: constrained transcript assembly of RNA-seq reads.
Song L, Florea L.
:: DESCRIPTION
SCARF is a next-gen sequence assembly tool for evolutionary genomics. Designed especially for assembling 454 EST sequences against high quality reference sequences from related species.
::DEVELOPER
The Dlugosch Lab @ The University of Arizona
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Feb 15;25(4):535-6. doi: 10.1093/bioinformatics/btp011. Epub 2009 Jan 6.
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.
Barker MS1, Dlugosch KM, Reddy AC, Amyotte SN, Rieseberg LH.
:: DESCRIPTION
Baa.pl is a simple script that parses the output of a BLAT run of a transcriptome vs. a genome assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
BugBuilder is a pipeline for the automated assembly and annotation of microbial genomes from high-throughput sequence data. It is configurable so as not to be tied to any assembler or scaffolder, and is designed to run in a cluster environment facilitating high-throughput processing of genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.
::DEVELOPER
The Chinese University of Hong Kong
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2009 Dec 24;10:447. doi: 10.1186/1471-2105-10-447.
Next generation transcriptomes for next generation genomes using est2assembly.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.
:: DESCRIPTION
Contrail is a Hadoop based genome assembler for assembling large genomes in the clouds
::DEVELOPER
Schatz Lab, Cold Spring Harbor Laboratory
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The BEAP is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as “primer”, to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the “primer” therefore help to “extend” the length of the original sequence for constructing a “full length” sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
James E. Koltes, Zhi-Liang Hu, Eric Fritz and James M. Reecy (2009).
BEAP: The BLAST Extension and Alignment Program — a tool for contig construction and analysis of preliminary genome sequence.
BMC Research Notes 2009, 2:11
:: DESCRIPTION
BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
Ergude Bao, Tao Jiang and Thomas Girke (2013)
Bioinformatics (2013) 29 (10): 1250-1259.doi: 10.1093/bioinformatics/btt127
