Contigs
jContigSort is is an useful Java-based instrument that was designed in order to help you sort genome contigs.
Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user.
Platforms: Windows
License: Freeware | Download (416): jContigSort Download |
A novel algorithm to layout the contigs with more than one reference genomes at a time using global searches
Platforms: Windows, Mac, BSD, Linux
License: Freeware | Size: 1.09 MB | Download (46): PGA Download |
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of...
Platforms: Mac
License: Freeware | Size: 1.06 MB | Download (39): Mugsy Download |
ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output...
Platforms: Mac
License: Freeware | Size: 61.44 KB | Download (38): ABACAS Download |
Using super-fast, integrated, high-performance computing algorithms, CLC Genomics Workbench sets a new standard for desktop based reference assembly and de novo assembly of SOLiD, Solexa, 454, and Helicos sequencing data# De novo assembly of Sanger, 454, Solexa, Helicos, and SOLiD data
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Platforms: Mac
License: Freeware | Size: 55 MB | Download (51): CLC Genomics Workbench for Mac OS Download |
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (49): JFinisher Download |
The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 822.6 KB | Download (56): Lightweight Genome Viewer (lwgv) Download |
POSA (Perl Objects for Sequence Analysis) provides an easy-to-use perl interface to handling raw ABI sequence trace files. For example: fasta can be extracted, sequence contigs can be build and putative SNPs and SBE primers can be easily generated.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 3.65 MB | Download (45): Perl Objects for Sequence Analysis Download |
The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the...
Platforms: Mac
License: Freeware | Size: 2.62 MB | Download (39): OSLay Download |