This milestone release is huge. It contains a lot of improvements and some important fixes. Here are some higlights: Features and improvements: #4, #15: The BLAST reference database and IDs mapping is now configurable #17: Added RNACentral reference DB (as the default one now) #18: BLAST options are now configurable #16: A dataflow API was improved and a pipeline without the Flash step was added #20 #24: For pipelines without Flash you can choose between FASTA and FASTQ input format Output tables improvements: #10: Added CSV-headers #19, #23, #27: Added taxonomic rank and name columns #6: Split each counts table on two: direct/accumulated #30: Zero direct counts are filtered out Important fixes: #28: Bio4j-NCBITaxonomy database was updated with an important fix for the taxonomic names #26: Ongoing effort to solve the "Too many open files" exception has been moved to ohnosequences/loquat#56 See the full list of pull requests merged in this release in the v1.0-M2 milestone.