Do you have Nanopaore or PacBio reads? Try minimap2 as a new aligner! From minimaps homepage:

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include:

• mapping PacBio or Oxford Nanopore genomic reads to the human genome
• finding overlaps between long reads with error rate up to ~15%
• splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome
• aligning Illumina single- or paired-end reads
• assembly-to-assembly alignment
• full-genome alignment between two closely related species with divergence below ~15%.

For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 preprint.

Read more in the minimap2 preprint from Heng Li - Minimap2: fast pairwise alignment for long nucleotide sequences.

Credits

Marius van den Beek for developing the Galaxy integration!