Looking for appropriate software

[lkral]

I currently have a number of undergraduate students annotating genes within scaffolds of a particular fish species using WebApollo. I also have Illumina NextSeq PE150 reads from a closely related species. To compare exon sequences between these species, it is easiest to simply align the NextSeq reads to the annotated scaffold. Currently I use Geneious to carry out this reference sequence alignment. However, each alignment takes 30 minutes to an hour and since I only have one floating license, tying it up for this length of time makes it difficult to schedule times for student to then extract/splice the exons and carry out alignments of the resulting coding sequences.

So, my question is this. Is anyone aware of a simple to use free/low cost software package that runs on desktop level hardware (I can't afford another $2,000 floating license) that carries out alignments of sequence reads to a reference sequence (usually in the 10kb to 15kb range) such that the aligned sequences can then be imported into Geneious?

[GenoMax]

BBMap should be easy to use on a desktop (PC/Mac) machine (hopefully you have at least 4 GB RAM available). As long as you can import SAM/BAM files into Geneious you would be all set.

[sphil]

can't this be done by basically every mapper which output bam/sam and is aware finding exon junctions?

[GenoMax]

The important bit in original post is "desktop level hardware" (i.e. limited hardware resources, most likely PC/Mac environment) and undergraduate students (though it is not clear if they are only doing annotation). It is easy to forget that small institutions (based on Ikral's location) have very limited resources (hardware/people) and majority of mappers are not designed for that demographic.

[lkral]

Thanks, GenoMax. That should do it. Geneious can import SAM/BAM files. I have a Mac with 8 GB of RAM that should be able to handle this.

And yes, we have limited computing resources. Also, to clarify, the student are currently doing only annotations, but now that I have sequences of a related species (soon two related species) they will be comparing the genes they annotate between the species looking for signs of adaptive variation within the protein coding regions.