Category: Assembly Tools

CAP3 / PCAP – Sequence and Genome Assembly Programs

CAP3 / PCAP

:: DESCRIPTION

CAP3 is a sequence assembly program for small-scale assembly of EST sequences with or without quality values.

PCAP is for large-scale assembly of genomic sequences with quality values and with or without forward-reverse read pairs.

::DEVELOPER

Xiaoqiu Huang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 CAP3 / PCAP

:: MORE INFORMATION

Citation:

Huang, X. and Madan, A. (1999)
CAP3: A DNA Sequence Assembly Program.
Genome Research, 9: 868-877.

Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
PCAP: A Whole-Genome Assembly Program.
Genome Research, 13: 2164-2170.

FPC 9.4 – Build Contigs from Fingerprinted Clones

FPC 9.4

:: 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

  • Linux/Windows

:: DOWNLOAD

 FPC

:: 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

SeqAssem 200807- Molecular Sequence Assembly

SeqAssem 200807

:: DESCRIPTION

SeqAssem is a molecular sequence assembly software, proof-reading of trace file data, contig building …..

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SeqAssem

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!

DNPTrapper 1.0 – Assembly Editing & Visualization Tool

DNPTrapper 1.0

:: DESCRIPTION

DNPTrapper, a shotgun sequence finishing tool, designed to address the key sequence assembly problems caused by repeated regions in a genome. The program detects and visualizes single nucleotide differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.

::DEVELOPER

Tammi Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

DNPTrapper

:: MORE INFORMATION

Citation:

BMC Bioinformatics, 2006 Mar 20; 7:155
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
Arner, E, Tammi, MT, Tran, AN, Kindlund, E, Andersson B.

SOMA 2.0 – Scaffolding using Optical Restriction Mapping

SOMA 2.0

:: DESCRIPTION

SOMA (Scaffolding using Optical Restriction Mapping) is a toolbox for finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome. Optical Maps are global, ordered maps of restriction site locations in a genome. This information can be quite useful in scaffolding contigs from a shotgun assembly to guide the finishing process.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SOMA

:: MORE INFORMATION

N/A

 

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