CHANGES IN VERSION 1.0.3 ----------------------- BUG FIXES o Fixed the memory leak in isBimeraDenovo and friends. o Sequence tables are now integer rather than numeric. CHANGES IN VERSION 1.0 ----------------------- NEW FEATURES o The dada2 package is now available from Bioconductor (http://bioconductor.org) CHANGES IN VERSION 0.99.9 ----------------------- NEW FEATURES o fastqFilter and fastqPairedFilter can now remove phiX contamination if rm.phix argument set to TRUE CHANGES IN VERSION 0.99.8 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o Banding in nwalign is now turned off by default BUG FIXES o Graceful handling of sequences which are not classified at any level by assignTaxonomy CHANGES IN VERSION 0.99.7 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o isBimera was rewritten in C, significantly increasing speed BUG FIXES o An edge case bimera detection bug was fixed CHANGES IN VERSION 0.99.6 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o Function documentation was reviewed and revised throughout the package CHANGES IN VERSION 0.99.5 ----------------------- NEW FEATURES o plotQualityProfile displays a visual summary of the quality scores over sequences in a fastq file o removeBimeraDenovo conveniently identifies and removes chimeras from the input unique sequences SIGNIFICANT USER-VISIBLE CHANGES o The dada2 package is now part of the devel branch of Bioconductor (http://bioconductor.org) BUG FIXES o assignTaxonomy now handles varying levels of taxonomic classification in the training data CHANGES IN VERSION 0.10.7 ----------------------- NEW FEATURES o dada2 now supports 454 pyrosequencing. When calling the dada function on 454 data, we recommend using the parameters USE_QUALS = FALSE, HOMOPOLYMER_GAP_PENALTY = -1, BAND_SIZE = 32 SIGNIFICANT USER-VISIBLE CHANGES o mergePairs is now "vectorized" over lists of input dada-class and derep-class objects o Added a homo_gap argument to nwalign which sets the homopolymer gap penalty in the N-W alignment BUG FIXES o assignTaxonomy now uses less memory