Alignment of Contigs.
Alignment of Reads
Denovo Sequence Assemblers
VELVET-Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
- MIRA-MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
- FORGE-Whole genome assembler that can combine heterogeneous DNA sequencing technologies. Uses MPI to scale across compute clusters.
- AMOS-Manipulation of input and output files related to whole-genome shotgun assembly.
- CLC Genomics Workbench-CLC bio supports the latest technological developments. And of course this includes the very interesting developments within Next Generation Sequencing (NGS).
- LaserGene-Comprehensive Software for DNA & Protein Sequence Analysis, Contig Assembly and Sequence Project Management - Now with expanded Next-Generation Sequence Assembly and Analysis Capability
- SeqMan NGen-Software for Next Generation sequence assembly of Illumina, Roche 454 Life Sciences, ABI SOLiD and Helicos Data
- SAM-SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.
inGAP-Integrated Next-gen Genome Analysis Platform
- DNA star-DNASTAR has software solutions to simplify your reference-guided assembly projects using Next-Generation Roche 454 Life Sciences, Illumina, ABI SOLiD, Helicos and/or Sanger data.
- MOSAIK- MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael StrBrmberg at Boston College. Win/Linux/MacOSX
- PASS- It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the
alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.