IDENTIFY

Locate - Unique description

What is the software called ?
- aTopHat2
What is a short description for this software ?
- TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. TopHat runs on Linux and OS X.
What are general categories (keywords, labels) for this software ?
Is there a project website for the software ?
- https://ccb.jhu.edu/software/tophat
[OPTIONAL] What is the DOI or any other unique identifier for this software (or software version) ?

UNDERSTAND

Trust - Quality and ratings

Who created this software? (Project, Organization, Person, Initiative, etc.)
- Cole Trapnell
Are there any additional contributors of note for this software ?
- Daehwan Kim
- Steven Salzberg
What useful features of this software are worth highlighting ?
[OPTIONAL] Who is the publisher of this software if not the author ?
[OPTIONAL] How can a user get support for the software ? (eg. Report bugs, request features and extensions, etc)
[OPTIONAL] Has the software been adopted in a project, organization or by a person?
[OPTIONAL] Is there any information about uses of this software (papers, research labs, etc) ?
[OPTIONAL] Are there any statistics of its use ?
[OPTIONAL] Are there any publications where the software is used ?
[OPTIONAL] Is there any benchmark information about the software ?
[OPTIONAL] What are the funding sources for this software?
[OPTIONAL] What are the ratings for this software?

Relate - Domain knowledge

What are domain specific keywords for this software ? (eg: hydrology, climate)
[OPTIONAL] Is there any other similar software that you know of ?
[OPTIONAL] What are the recommended uses and assumptions for the software ?
[OPTIONAL] Are there any constraints on use, situations it is not designed for, simplifications ?

EXECUTE

Access - Download

What is the URL for the code ?
- https://github.com/infphilo/tophat
What license is the code released under ?
- Boost Software License, Version 1.0
[OPTIONAL] Is there a URL for the executable ?
- https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

Install - Execution requirements

Is there any on-line documentation about the software ?
What language(s) is the software written in ?
What Operating Systems can the software run on ?
How can one install the software ?
What other software does the software require to be installed ?
[OPTIONAL] Are there estimates of how long it takes to run this software on average ?
[OPTIONAL] Are there any memory requirements for this software ?
[OPTIONAL] Are there any other important details about the implementation of this code (parallelization, special hardware, etc) ?

Run - Testing execution

Is there any test data available for the software ?
[OPTIONAL] Are there any specific instructions for testing the software ?

DO RESEARCH

Experiment - Run with other data

What input files does the software require ?
- - File Id:
    inputZippedFASTQ
  - File Type:
    1 zip file for 1 component-run. >1 Fastq files can exist for 1 sample and need to be analyzed together. So we zip the files so we have 1:1 mapping for files - sample.
- - File Id:
    refFastaBundle
  - File Type:
    Zip file with bowtie2 indices and fasta files. The indices and fasta file, fasts-index file need to be in the same directory for Tophat2 to run smoothly
- - File Id:
    tophat2Params
  - File Type:
    json/xml file with TopHat2 parameters are input. There are way too many parameters. Adding each parameter to the component might make it look very messy.
What are the input parameters used for this software?
What output files does the software produce ?
- - File Id:
    alignedBAM
  - File Type:
    Fastq file aligned with reference human genome results in BAM files (binary alignment format). The aligned/mapped file contains sequences/alignments that were successfully aligned to the human reference genome
- - File Id:
    unmappedBAM
  - File Type:
    Any sequences that were not mapped to human reference genome are dumped into unmappedBAM by bowtie2 and tophat2.
- - File Id:
    junBED
  - File Type:
    Track of junctions reported by TopHat2. Specific to splice junctions for RNASeq file
- - File Id:
    insertionsBED
  - File Type:
    Track of insertions (mutations) reported by TopHat2
- - File Id:
    deletionsBED
  - File Type:
    Track of deletions (mutations) reported by TopHat2
[OPTIONAL] Are there any relevant data catalogs that can be used with this software ?

Compose - Run with other software

What other software can interoperate with this one?
[OPTIONAL] Is this software typically used with other software in a workflow ? (eg: for visualization, preprocessing, postprocessing, etc)

Cite - Scientific publications

Is there a preferred publication or citation for this software ?
- - Citation Text:
    Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R. and Salzberg S. “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions”. Ge-nome Biology. 14:R36. 2013.
  - Citation Location:
    https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-4-r36

TopHat2 [ Cole Trapnell]

IDENTIFY

Locate - Unique description

UNDERSTAND

Trust - Quality and ratings

Relate - Domain knowledge

EXECUTE

Access - Download

Install - Execution requirements

Run - Testing execution

DO RESEARCH

Experiment - Run with other data

Compose - Run with other software

Cite - Scientific publications

GET SUPPORT

Discuss - Support and community

UPDATE

Contribute - Evolution

Track - Versions