Hobbes is a software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). Hobbes accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.
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BMC Bioinformatics. 2014 Feb 5;15:42. doi: 10.1186/1471-2105-15-42.
Improving read mapping using additional prefix grams.
Kim J, Li C, Xie X
Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.
Hobbes: optimized gram-based methods for efficient read alignment.
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.