DNA Sequence Assembly Software

2015-01-13

azim58 - DNA Sequence Assembly Software

DNA Sequence Assembly
Contig Assembly
Sequence Alignment Software
good free software for assembling dna sequences

see
-http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Alignment_Viewers.2FEditors
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DNA Baser
-I think this is one of the most user friendly sequence alignment tools I have seen.
-the price is $60 per month or less if you pay for multiple months

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-CLC workbench
--they require you to request a quote or pay about $79 as a student.  To download the free trial you have to fill out a form.

free and open source assembly programs
http://sequenceassembly.com/

-UGENE
--this software looks quite good maybe. . I tried to do a few things with it for a short time, but I had some trouble.
--UGENE can open ab1 chromatograms (just open a chromatogram file).  Select sequence by right clicking and select sequence region

Base-by-Base (Base by Base)
--This software looks quite good as well.  It looks like it just runs in the browser with Java which could be a problem in certain situations.

Gap4 / Gap5
 Open source sequence assembler for Sanger sequencing. Part of the Staden
package of DNA sequence analysis tools.

Phrap
 The sequence assembly program Phrap was developed to assemble shotgun
cosmid and BAC sequencing projects in the Human Genome Project. Phrap
pioneered a number of important idea, including the automatic use of
entire sequences without trimming and accurate consensus sequences based
on sequence qualities and confirmation by other reads.

BAli-Phy
-doesn't seem to have any type of gui

DECIPHER
-an R Bioconductor package

Free for academic research use.

Celera Assembler
 The program that was used to assemble the first human genome, released
as open source in 2004. Assembles Sanger sequencing data and Roche 454
data.

Arachne
 A whole genome assembler for Sanger sequencing reads developed at the
Broad Institute. Free for research and educational use.

ALLPATH
 A sequence assembly program for whole genome assemblies from short
("next generation") sequencing reads from MIT's Broad Institute. Free for
research and educational use.

MUMmer
 An open source software package for aligning whole genomes.

AMOS
 A Modular, Open Source whole genome assembler. A collaboration of four
research institutes.

The Sanger Institute also has software to download
http://www.sanger.ac.uk/resources/software/

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see also
http://en.wikipedia.org/wiki/Sequence_assembly#Available_assemblers

Here's a paper about sequence assembly
Sequence assembly demystified
http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3367.html?WT.mc_id=
TWT_NatureRevGenet