TransLig is an efficient genome-guided trascriptome assembler for RNA-seq data. It can assemble all transcripts from short paired-end reads using a reference genome and analyze their abundances. The software expects as input alignment file by Tophat2 BAM format, and ouput all assembled candidate transcripts in gtf format.
module add translig-1.3 Assemble [--reads/--kmers] <filename> [opts]
This software is free, open-source software released under the GNU General Public License.