:: DESCRIPTION
Admix’em (Admixture simulator) is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Admix’em: A flexible framework for forward-time simulations of hybrid populations with selection and mate choice.
Cui R, Schumer M, Rosenthal GG.
Bioinformatics. 2015 Nov 28. pii: btv700.
:: DESCRIPTION
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ragout-a reference-assisted assembly tool for bacterial genomes.
Kolmogorov M, Raney B, Paten B, Pham S.
Bioinformatics. 2014 Jun 15;30(12):i302-i309. doi: 10.1093/bioinformatics/btu280.
:: DESCRIPTION
ABRA is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ABRA: improved coding indel detection via assembly based re-alignment.
Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.
Bioinformatics. 2014 Jun 6. pii: btu376
:: DESCRIPTION
NOmESS is a homolgy-driven assembly tool to create a NOn-redundant protEin Sequence Set for mass spectrometry.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Homology-driven assembly of NOn-redundant protEin Sequence Sets (NOmESS) for mass spectrometry.
Temu T, Mann M, Räschle M, Cox J.
Bioinformatics. 2016 Jan 6. pii: btv756.
:: DESCRIPTION
CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy-to-learn user interface.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Metassembler is a software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2015 Sep 24;16:207. doi: 10.1186/s13059-015-0764-4.
Metassembler: merging and optimizing de novo genome assemblies.
Wences AH, Schatz MC
:: DESCRIPTION
pilon uses read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM.
PLoS One. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963.
:: DESCRIPTION
Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The phusion assembler.
Mullikin JC and Ning Z
Genome research2003;13;1;81-90
:: DESCRIPTION
MindTheGap is a software that performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
MindTheGap : integrated detection and assembly of short and long insertions.
Rizk G, Gouin A, Chikhi R, Lemaitre C.
Bioinformatics. 2014 Aug 14. pii: btu545
:: DESCRIPTION
IsoSCM (Isoform Structural Change Model) is a new method for transcript assembly that incorporates change-point analysis to improve the 3′ UTR annotation process.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
RNA. 2015 Jan;21(1):14-27. doi: 10.1261/rna.046037.114. Epub 2014 Nov 18.
IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference.
Shenker S, Miura P, Sanfilippo P, Lai EC
