I assume you have the reference genome sequence for your transcripts..

In that case, instead of "assembling" it is better to "align" those transcripts to your reference genome. A good and fast tool for this is Bowtie (http://bowtie-bio.sourceforge.net/index.shtml), for example.

If there is no reference genome sequence available, then a "de-novo" assembling is necessary, and a tool for this is Trinity assembler (https://github.com/trinityrnaseq/trinityrnaseq/wiki)

Best regards.

RNA-Seq analysis - Transcriptome assembly and differential expression

http://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/rna-sequencing/rna-seq-analysis-transcripto-0

Full-length transcriptome assembly from RNA-Seq data without a reference genome

http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html

Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742321/pdf/gni-13-119.pdf

BBmap can be an option. https://publications.lbl.gov/islandora/object/ir%3A1005301. It is capable of handling both splice junctions and the Ion Torrent's indel-containing error profile. To read http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-264

Thank You Dear Salvador Ramirez-Flandes, Jetty Ramadevi and A K M Firoj Mahmud for your valuable suggestions.