Most commonly used scientific software (bioinformatics/analysis/etc)

Question

[mbparsa]

Hi Biostars,

I am looking for an open source software that has been widely used in the past and current with biologist, I am a software graduate student and my main focus is on scientific software testing. Greatly appreciate if you can name some of the open source commonly used software in your community?

Edit: So the main purpose of this query "Finding the most commonly used software" is to run some software tests on source code and see if we can help and improve open source software.

[Eva_Maria]

1. Blast
2. Velvet
3. BWA
4. Bowtie
5. Tophat
6. cufflinks,cuffmerge,cuffdiff
7. Orthomcl
8. Muscle
9. Spine/AGEnt
10. WEKA / SVM

Answer 1

[Michael]

1. BLAST

Have a look at the Biostars tags: https://www.biostars.org/t/ and try to extract only those tags which are software:

Then you get

1. R ahead of
2. Python
3. blast
4. samtools
5. Biopython

But R and Python are also programming languages (and have an 'unfair advantage') which you can do a lot of different things with, therefore blast is - not surprisingly - the tool Biostars' users have most questions about.

[mbparsa]

Thanks Michael, can you give me a list of top 10 that you use in regular base ?

[mbparsa]

Also, I could not find a similar question in the other pages. I am only looking for a top most commonly used software in the community. Would you please reconsider opening this post?

[Michael]

Sorry, I closed this by mistake, it is open. I would consider using the Biostar tags also as another source of input. My usage is definitely not representative.

Answer 2

[cbio]

There are many different software packages for many different things in Bioinformatics.

• Bowtie
• Bowtie2
• Tophat
• MACS2
• SICER
• HOMER
• Samtools
• Picardtools
• Deeptools
• Bamtools
• Biobambam
• NGSPLOT

and tons of varying packages in R.

[mbparsa]

Thanks Snoopy,

If you would wanna make a top 5 or top 10 , would you consider the current list or change it?

How about Galaxy, Blast etc?

[cbio]

The top 5 software tools I use are different between mapping software and the top 5 differential expression software tools I use and etc.

I prefer command line tools so I don't use Galaxy, and I don't use blast very often but I know it's very popular.

Answer 3

[dariober]

To add one more data point to your survey, here's my selection from top of my head

• samtools
• bedtools
• bwa
• tophat
• igv
• macs (peak caller)
• cutadapt
• edgeR/limma
• blast

I deliberately left out general purpose tools like R, python, unix command line tools etc.

Answer 4

[SES]

Take a look a the Nature's top 100 for a historical view: http://www.nature.com/news/the-top-100-papers-1.16224

Interestingly, the Clustal W paper is ranked above BLAST, though there are several BLAST and Clustal papers so I think BLAST is collectively higher. Either way, both have had a large impact on the field but timing is a major factor in popularity, especially in the citation statistic.

[mbparsa]

Thanks SES, that was really useful. I also looked at this which I found it quite surprising! "top cited in bioinformatics journal"