Mining RNA-seq data for infections and contaminations. by Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C Friedel

“…In particular, ContextMap vastly outperformed GASiC and GRAMMy in terms of runtime. In contrast to MEGAN4, it was capable of providing individual read mappings to species and resolving non-unique mappings, thus allowing the identification of misalignments caused by sequence similarities between genomes and missing genome sequences. …”
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