App Name	CyVerse Platform	Third-party Documentation	CyVerse Documentation	Estimated Runtime for Sample Data Set	Link to App
FastQC	DE	http://www.bioinformatics. babraham.ac.uk/projects/fastqc/   https://www.youtube.com/watch?v=bz93ReOv87Y	https://wiki.cyverse.org/wiki/pages/viewpage.action?pageId=9316768	15 min	https://de.iplantcollaborative. org/de/?type=apps&app-id=112b9aa8-c4a7-11e5-8209- 5f3310948295
Trimmomatic v0.33	DE	https://github.com/timflutre/trimmomatic	https://wiki.cyverse.org/wiki/display/DEapps/Trimmomatic-programmable-0.33	30 min	https://de.iplantcollaborative. org/de/?type=apps&app-id=9c2a30dc-028d- 11e6-a915-ab4311791e69
Sickle	DE	https://github.com/najoshi/sickle	https://wiki.cyverse.org/wiki/display/DEapps/Sickle-quality-based-trimming	30 min	https://de.iplantcollaborative. org/de/?type=apps&app-id=68b278f8-d4d6-414d-9a64-b685a7714f7c
Trinity	Atmosphere	https://github.com/trinityrnaseq/trinityrnaseq/wiki	https://pods.iplantcollaborative. org/wiki/display/atmman/Trinity+-+Trinotate+Atmosphere+Image	1 week	https://atmo.iplantcollaborative. org/application/images/1261
	DE		https://wiki.cyverse.org/wiki/display/DEapps/Trinity-64GB-2.1.1	2-5 days	https://wiki.cyverse.org/wiki/display/DEapps/Trinity-64GB-2.1.1
rnaQUAST v1.2.0	DE, Atmosphere	http://spades.bioinf.spbau.ru/rnaquast/release1.2.0/manual.html	https://pods.iplantcollaborative. org/wiki/display/TUT/rnaQUAST+1.2.0+%28denovo+based%29+using+DE	30 min	https://de.iplantcollaborative. org/de/?type=apps&app-id=980dd11a-1666- 11e6-9122-930 ba8f23352
Transdecoder	DE	https://transdecoder.github.io	https://wiki.cyverse.org/wiki/display/DEapps/Transcript+decoder+2.0	2-3 hours	https://de.iplantcollaborative. org/de/?type=apps&app-id=5a0ba87e-b0fa-4994-92a2- 0d48ee881179
DESeq2	DE	https://bioconductor.org/packages/release/bioc/html/DESeq2.html	https://pods.iplantcollaborative. org/wiki/pages/viewpage.action?pageId=28115142	2-3 hours	https://de.iplantcollaborative. org/de/?type=apps&app-id=9574e87c-4f90- 11e6-a594-008 cfa5ae621
EdgeR	DE	https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeR.pdf	https://wiki.cyverse.org/wiki/pages/viewpage.action?pageId=28115144	2-3 hours	https://de.iplantcollaborative. org/de/?type=apps&app-id=4a08ceda-54fe- 11e6-862f-008 cfa5ae621
Trinotate	Atmosphere	https://trinotate.github.io/	https://pods.iplantcollaborative. org/wiki/display/atmman/Trinity+-+Trinotate+Atmosphere+Image	1 week	https://atmo.iplantcollaborative. org/application/images/1261