Im working with de novo assembly of small genomes and 16s metagenomics. I need to perform constant analyses of genome data, but it is frustrating to renew the expensive license of the software year by year, because there are times that I dont have enough funds to renew the license. I want to pay just one time for the unlimited use of any useful software. Any suggestions please?.
Is this exclusively Illumina data? If so, does their free cloud solution (Illumina "BaseSpace") offer what you need?
http://www.illumina.com/informatics/basespace/basespace-app-store.ilmn
Or what about the countless open source tools? Search through some of the accumulated lists of free, open source tools to see if what you need is there? e.g. http://seqanswers.com/wiki/Software
Or from places like the Broad Insitute - http://www.broadinstitute.org/scientific-community/software (e.g. Galaxy - http://galaxyproject.org ).
Many people never pay one cent for commercial software and do everything with open source tools. Biocoductor and R are another valuable resource for NGS tools.
It can take some searching to find what you need, but odds are very likely that whatever you wish to do, there is a free tool to do it. You may find you need to master some basic command line Linux, as much of the open source tools are command line tools (although not all by any means, and even many Linux tools have been ported to Windows by someone else at some time).
If you have a Linux machine available, you may want to consider converting it to BioLinux, which is based on Ubuntu, and is one project's attempt to provide a full suite of genomics tools in a single fully integrated, ready to use Linux distribution - http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
Is this exclusively Illumina data? If so, does their free cloud solution (Illumina "BaseSpace") offer what you need?
http://www.illumina.com/informatics/basespace/basespace-app-store.ilmn
Or what about the countless open source tools? Search through some of the accumulated lists of free, open source tools to see if what you need is there? e.g. http://seqanswers.com/wiki/Software
Or from places like the Broad Insitute - http://www.broadinstitute.org/scientific-community/software (e.g. Galaxy - http://galaxyproject.org ).
Many people never pay one cent for commercial software and do everything with open source tools. Biocoductor and R are another valuable resource for NGS tools.
It can take some searching to find what you need, but odds are very likely that whatever you wish to do, there is a free tool to do it. You may find you need to master some basic command line Linux, as much of the open source tools are command line tools (although not all by any means, and even many Linux tools have been ported to Windows by someone else at some time).
If you have a Linux machine available, you may want to consider converting it to BioLinux, which is based on Ubuntu, and is one project's attempt to provide a full suite of genomics tools in a single fully integrated, ready to use Linux distribution - http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
Here is some comparison (might be useful):
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017915
Bioconductor packages (free) :
http://www.ebi.ac.uk/training/sites/ebi.ac.uk.training/files/materials/2013/131021_HTS/genesandgenomes.pdf
http://www.bioconductor.org/help/course-materials/2011/SeattleIntro2011/Bioconductor-tutorial.pdf
I know there is a much reading there, but I hope you find some useful clues there
Margaret
The best (newest, updated, best for high-throughput) bioinformatics software is free (as the best things in life are free :) )
This is because only the global research community can be "cutting edge".
For de-novo, you can go eg. for SOAPdenovo or Trinity.
It will require some IT admin tasks for the installation, but also commercial software reqires effort for that too.
I agree with Michael, that BioLinux is great. I worked with these distro, what I love is numerous biological packages already installed and working. Here are the link to packages and instructions how to add it to Ubuntu:
http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository
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