:: DESCRIPTION
ConPADE is a tool used to estimate contig ploidy and allele dosage in polyploid genome assemblies.
::DEVELOPER
Microsoft Computational Biology Tools
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Margarido GR, Heckerman D.
ConPADE: genome assembly ploidy estimation from next-generation sequencing data.
PLoS Comput Biol. 2015 Apr 16;11(4):e1004229. doi: 10.1371/journal.pcbi.1004229. PMID: 25880203; PMCID: PMC4400156.
:: DESCRIPTION
GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
GMvalue is a tool to determine misassembly sites in contigs and scaffolds.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.
Kosugi S, Hirakawa H, Tabata S.
Bioinformatics. 2015 Aug 10. pii: btv465.
:: DESCRIPTION
Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Source Code Biol Med. 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23.
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG1, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.
:: DESCRIPTION
Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.
::DEVELOPER
Human Genome Sequencing Center, Baylor College of Medicine
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MIP Scaffolder is a program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2011 Dec 1;27(23):3259-65. Epub 2011 Oct 13.
Fast scaffolding with small independent mixed integer programs.
Salmela L, Mäkinen V, Välimäki, N, Ylinen J, Ukkonen E.
:: DESCRIPTION
DNA Dragon Contig Assembler assembles sequences, trace data (ABI, SCF, AB1), Illumina and Roche 454 flowgrams into contigs. It is a very fast and accurate DNA sequence assembly software. The DNA sequences are assembled into contigs and a direct comparision of trace date with nucleotide data is possible. It also allows for proofreading and base editing.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Multifasta Analysis is used to get informations(N50, max contig, min, amount, amount of bases) about a set of contigs
::DEVELOPER
Prof. Rommel Ramos
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Simplifier is a stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes.
::DEVELOPER
Prof. Rommel Ramos
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformation. 2012;8(20):996-9. doi: 10.6026/97320630008996. Epub 2012 Oct 13.
Simplifier: a web tool to eliminate redundant NGS contigs.
Ramos RT, Carneiro AR, Azevedo V, Schneider MP, Barh D, Silva A.
:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
FPC (fingerprinted contigs)is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments.FPC has an algorithm to automatically cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap. FPC has editing facilities for the user to refine the coordinates and to remove poorly fingerprinted clones. Functions are available for updating an FPC database with new clones. Contigs can easily be merged, split or deleted. Markers can be added to clones and are displayed with the appropriate contig. Sequence ready clones can be selected and their sequencing status displayed. As such, FPC is an integrated program for the assembly of sequence ready clones for large scale sequencing projects
:: DEVELOPER
Arizona Genomics Computational Lab (AGCoL)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nelson, W. and C. Soderlund (2009).
Integrating Sequence with FPC Fingerprinted Maps.
Nucleic Acids Research 1-11 doi:10.1093/nar/gkp034
