MAQ
Maq (Mapping and Assembly with Quality) is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Maq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find... [Read More...]
VELVET
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs European Bioinformatics Institute have developed a new set of algorithms, collectively called “Velvet,” to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25–50 bp) data sets. Applying Velvet to very short reads and... [Read More...]
SSAKE
The Short Sequence Assembly by K-mer search and 3′ read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3′-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. SSAKE is written... [Read More...]
VCAKE
VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina’s Solexa Sequencing data. More Information Webpage: http://vcake.sourceforge.net/ CIP User: Jan Kreuze, Wilmer Cuellar Read More →
TGICL
This package automates clustering and assembly of a large EST/mRNA dataset. The clustering is performed by a slightly modified version of NCBI’s megablast , and the resulting clusters are then assembled using CAP3 assembly program. TGICL starts with a large multi-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3. Both clustering and assembly phases can be parallelized... [Read More...]
MIRA 3
MIRA 3 – Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina MIRA is the swiss army knife of sequence assembly that I’ve used and developed during the past 10 years to get assembly jobs I work on done efficiently – and especially accurately. That is, without me actually putting too much manual work into it. Over time, other labs and sequencing providers have found mira useful for assembly of extremely... [Read More...]
CAP3
We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 58 and 38 low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly... [Read More...]
SeqClean
A script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. More Information Webpage: http://compbio.dfci.harvard.edu/tgi/software/ CIP User: Roland Schafleitner, Rosalina Tincopa Read More →
Repeatmasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence... [Read More...]
Annotation of Sequences
Blast2GO Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features a: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are automatic. User-friendly. Blast2GO is designed for experimentalists. An intuitive interface, the many graphical parameters and the detailed users manual makes... [Read More...]