10.01.2012
AllPaths-LG

ALLPATHS-LG is a whole genome shotgun assembler that can generate
high quality genome assemblies using short reads (~100bp) such as those produced
by the new generation of sequencers. The significant difference between ALLPATHS
and traditional assemblers such as Arachne is that ALLPATHS assemblies are not
necessarily linear, but instead are presented in the form of a graph. This graph
representation retains ambiguities, such as those arising from polymorphism,
uncorrected read errors, and unresolved repeats, thereby providing information
that has been absent from previous genome assemblies.
https://www.msi.umn.edu/sw/Allpath
Category: Assembly
02.09.2010
cap3

CAP3 is a sequence assembly program for DNA sequence
with or without quality values.
http://seq.cs.iastate.edu/
Category: Assembly
02.01.2012
euler

Euler is a new approach to fragment assembly that abandons the
classical "overlap - layout - consensus" paradigm that is used in all currently
available assembly tools.
http://nbcr.sdsc.edu/euler/
Category: Assembly
02.09.2010
euler-SR

EULER-SR is a program for de novo assembly of reads (from Roche 454
Live Sciences or Illumina/Solexa).
http://ngslib.i-med.ac.at/node/64
Category: Assembly
17.02.2012
FLASH

FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast
tool to merge paired-end reads from fragments that are shorter than twice the
length of reads. The extended length of reads has a significant positive impact
on improvement of genome assemblies.
http://www.cbcb.umd.edu/software/flash
Category: Assembly
31.07.2012
GapCloser
The GapCloser is designed to close the
gaps emerging during the scaffolding process by SOAPdenovo, using the abundant
pair relationships of short reads.
http://soap.genomics.org.cn/about.html#resource2
Category: Assembly
02.09.2010
maq

Maq 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.
http://maq.sourceforge.net/maq-man.shtml
Category: Assembly
12.06.2013
MaSuRCA

MaSuRCA is whole genome assembly software. It combines the efficiency
of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA
can assemble data sets containing only short reads from Illumina sequencing or a
mixture of short reads and long reads (Sanger, 454)
http://www.genome.umd.edu/masurca.html
Category: Assembly
02.09.2010
newbler

Newbler is a software package for de novo DNA sequence assembly. It
is designed specifically for assembling sequence data generated by the 454
GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche
diagnostic.
http://en.wikipedia.org/wiki/Newbler
Category: Assembly
02.09.2010
oases

Oases is a de novo transcriptome assembler designed to produce
transcripts from short read sequencing technologies, such as Illumina, SOLiD, or
454 in the absence of any genomic assembly. It was developed by Marcel Schulz
(MPI for Molecular Genomics) and Daniel Zerbino (previously at the European
Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz).
Oases
uploads a preliminary assembly produced by Velvet, and clusters the contigs into
small groups, called loci. It then exploits the paired-end read and long read
information, when available, to construct transcript isoforms.
http://www.ebi.ac.uk/~zerbino/oases/
Category: Assembly
03.10.2012
OSLay

A new tool OSLay that uses synteny between matching sequences in a
target assembly and a reference assembly to layout the contigs (or scaffolds) in
the target assembly. The tool provides an interactive visualization of the
computed layout and the result can be imported into the assembly editing tool
Consed to support the design of primer pairs for gap-closure.
http://ab.inf.uni-tuebingen.de/software/oslay/
Category: Assembly
29.11.2012
PASA

PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome
annotation tool that exploits spliced alignments of expressed transcript
sequences to automatically model gene structures, and to maintain gene structure
annotation consistent with the most recently available experimental sequence
data. PASA also identifies and classifies all splicing variations supported by
the transcript alignments.
http://pasa.sourceforge.net/
Category: Annotation , Assembly
03.09.2010
pcap
Parallel Contig Assembly Program (PCAP) assemble the data produced by a
whole-genome shotgun sequencing project.
http://seq.cs.iastate.edu/
Category: Assembly
02.09.2010
phrep / phrap

The phred software reads DNA sequencing trace files, calls bases, and
assigns a quality value to each called base. Phrap is a program for assembling
shotgun DNA sequence data.
http://www.phrap.org/phredphrapconsed.html
Category: Assembly
14.06.2011
Ray

Parallel genome assemblies for parallel DNA sequencing. Ray is a parallel
software that computes
de novo genome assemblies with next-generation
sequencing data. Ray is written in C++ and can run in parallel on numerous
interconnected computers using the message-passing interface (MPI) standard.
http://denovoassembler.sourceforge.net/
Category: Assembly
16.05.2014
SGA

SGA is a de novo genome assembler based on the concept of string graphs. The
major goal of SGA is to be very memory efficient, which is achieved by using a
compressed representation of DNA sequence reads.
https://github.com/jts/sga
Category: Assembly
28.03.2013
ShoRAH

ShoRAH is a software package that allows for inference about the
structure of a population from a set of short sequence reads as obtained from
ultra-deep sequencing of a mixed sample.
http://www.bsse.ethz.ch/cbg/software/shorah
Category: Assembly
31.07.2012
SOAPdenovo
SOAPdenovo is a novel short-read assembly method that can build
a de novo draft assembly for the human-sized genomes. The program is specially
designed to assemble Illumina GA short reads. It creates new opportunities for
building reference sequences and carrying out accurate analyses of unexplored
genomes in a cost effective way.
http://soap.genomics.org.cn/soapdenovo.html
Category: Assembly
17.02.2012
SOAPdenovo-trans

SOAPdenovo-Trans is a de novo transcriptome assembler basing
on the SOAPdenovo framework, adapt to alternative splicing and different
expression level among transcripts.The assembler provides a more accurate,
complete and faster way to construct the full-length transcript sets.
http://soap.genomics.org.cn/SOAPdenovo-Trans.htm
Category: Assembly
02.09.2010
ssaha

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a
pairwise sequence alignment program designed for the efficient mapping of
sequencing reads onto genomic reference sequences.
http://www.sanger.ac.uk/resources/software/ssaha2/
Category: Assembly
02.08.2012
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.
http://compbio.dfci.harvard.edu/tgi/software/
Category: Assembly
02.08.2012
trans-ABYSS

Trans-ABySS is a software pipeline for analyzing ABySS-assembled
contigs from shotgun transcriptome data. The pipeline accepts assemblies that
were generated across a wide range of k values in order to address variable
transcript expression levels. It first filters and merges the multi-k
assemblies, generating a much smaller set of nonredundant contigs. It contains
scripts that map assembled contigs to known transcripts, currently supporting
the Blat contig-to-genome aligner. It identifies novel splicing events like
exon-skipping, novel exons, retained introns, novel introns, and alternative
splicing. Its scripts can also identify candidate gene-fusions,
single-nucleotide variants, insertions, deletions, and inversions.
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/
Category: Assembly
02.08.2012
trinityrnaseq
Trinity, developed at the Broad Institute and the Hebrew
University of Jerusalem, represents a novel method for the efficient and robust
de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines
three independent software modules: Inchworm, Chrysalis, and Butterfly, applied
sequentially to process large volumes of RNA-seq reads. Trinity partitions the
sequence data into many individual de Bruijn graphs, each representing the
transcriptional complexity at at a given gene or locus, and then processes each
graph independently to extract full-length splicing isoforms and to tease apart
transcripts derived from paralogous genes.
http://trinityrnaseq.sourceforge.net/
Category: Assembly
17.12.2013
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.
http://vcake.sourceforge.net/
Category: Assembly
02.09.2010
velvet

Velvet is a de novo genomic assembler specially designed for short
read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
Cambridge, in the United Kingdom.
Velvet currently takes in short read
sequences, removes errors then produces high quality unique contigs. It then
uses paired-end read and long read information, when available, to retrieve the
repeated areas between contigs.
http://www.ebi.ac.uk/~zerbino/velvet/
Category: Assembly
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