Question: Most commonly used scientific software (bioinformatics/analysis/etc)
1
gravatar for mbparsa
3.2 years ago by
mbparsa10
mbparsa10 wrote:

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. 

R software error • 1.0k views
ADD COMMENTlink modified 3.2 years ago by dariober10.0k • written 3.2 years ago by mbparsa10
1

1. Blast

2. Velvet

3. BWA

4.Bowtie

5.Tophat

6. cufflinks,cuffmerge,cuffdiff

7.Orthomcl

8.Muscle

9.Spine/AGEnt

10. WEKA / SVM

ADD REPLYlink written 3.2 years ago by akhilvbioinfo130
3
gravatar for Michael Dondrup
3.2 years ago by
Bergen, Norway
Michael Dondrup46k wrote:
  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. 

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Michael Dondrup46k

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

ADD REPLYlink written 3.2 years ago by mbparsa10

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?

ADD REPLYlink written 3.2 years ago by mbparsa10
1

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Michael Dondrup46k
2
gravatar for cbio
3.2 years ago by
cbio400
cbio400 wrote:

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.

ADD COMMENTlink written 3.2 years ago by cbio400

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?

ADD REPLYlink written 3.2 years ago by mbparsa10

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.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by cbio400
2
gravatar for dariober
3.2 years ago by
dariober10.0k
WCIP | Glasgow | UK
dariober10.0k wrote:

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. 

ADD COMMENTlink written 3.2 years ago by dariober10.0k
1
gravatar for SES
3.2 years ago by
SES8.2k
Vancouver, BC
SES8.2k wrote:

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.

ADD COMMENTlink written 3.2 years ago by SES8.2k

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

ADD REPLYlink written 3.2 years ago by mbparsa10
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