I am looking for a command-line tool that can do something I've been doing in a low-throughput manner using Geneious. I have very fragmented de novo transcriptome assemblies, and what I've been able to do is retrieve short reads from my sequencing output that map to fragmented assemblies and then build up a more complete assembly using Geneious' "map to reference" command, which iterates and maps the reads to the reference, building outward from the ends of the fragments as far as the reads allow.
I have tried doing something similar with Bowtie2 and SamTools, but Bowtie doesn't seem to do much in the way of mapping outward from the ends of my fragmented reference sequence, even if I add N's to the ends of the sequence, and I don't think there is a way to tell Bowtie to try to iterate and extend the assembly (I could be mistaken about that). Does anyone know of a command line tool that could accomplish this, or of a way to get Bowtie to work for this?
Thanks very much!