Novel miRNA identification

Question

[tesic93]

Hi!

What are some good open-licensed tools for novel miRNA identification from miRNA-Seq files? I've combed trough tools4mirs.org, but I haven't found something that suits my usecase, since most of them are either dependent on miRDeep2, which is licensed, or aren't quite what I need. I need a tool that has the following feartures:

• can be used for human sequences

• can identify novel mature miRNA sequences

• can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

• has a license that allows non-academic use of the tool

• doesn't require usage of GUI

Thanks,

Nikola

[Friederike]

or aren't quite what I need

can you specify a bit more what your specific needs are?

[tesic93]

Sorry, I should have been clearer with the question. I need a tool that can do the following:

• can be used for human sequences

• can identify novel mature miRNA sequences

• can handle input read that have miRNA-Seq experimental strategy (but tools that can handle input files with other experimental strategies would be useful as well)

• has a license that allows non-academic use of the tool

Thanks!

Nikola

[Friederike]

you could edit your initial question to include all those details

[tesic93]

Thanks, I've included that in the initial question.

[h.mon]

Aren't sRNAbench or CAP-miRSEQ suitable?

[tesic93]

sRNAbench can't be downloaded from their website as far as I know, they had a server crash from which they didn't recover fully.

CAP-miRSEQ seems to use miRDeep2 for alignment, so I can't use it because of miRDeep's academic-only license.

[h.mon]

Link to sRNAbench stand-alone jar:

http://bioinfo2.ugr.es/sRNAtoolboxDB/exec/sRNAbench.jar

[tesic93]

Thanks! I'll try using sRNAbench then.

Answer 1

[Buffo]

miRDeep2 is probably the most common software to perform it.

[GenoMax]

OP has indicated that that program is not suitable for their purpose due to licensing restrictions.

[h.mon]

In the meantime (on October 16, 2018), miRDeep2 authors added the GNU GPL version 3 to the github repository, so it is now compatible with non-academic use.

Answer 2

[brianj.park]

You can also give miRge2.0 a try.