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?
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?
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