CHANGES IN VERSION 1.2.0
-----------------------

NEW FEATURES

    o Multithreading. The dada function is now multithreaded. This behavior is controlled by the multithread argument to the function and is FALSE by default: dada(..., multithread=FALSE/TRUE). Multithreaded chimera detection is also available and activated similarly: removeBimeraDenovo(..., multithread=FALSE/TRUE).

    o Species-level taxonomic assignment. The new assignSpecies function uses exact matching to assign sequences to the species level. Training fastas for species assignment are currently available for the Silva and RDP taxonomic databases.
    
    o Consensus-based chimera detection. isBimeraDenovoTable is a new method for detecting chimeras on multi-sample sequence tables. It first identifies bimeras on a per-sample basis, and then uses a consensus-across-samples approach to identify chimeric sequences. This improves the specificity of chimera classification for datasets with many samples. This method is also available through the convenience interface removeBimeraDenovo(..., tableMethod="consensus").
    
SIGNIFICANT USER-VISIBLE CHANGES

    o The vectorized aligner has been updated. It is now more flexible, handling different length sequences and variable end-gap penalties. It is also faster: On default settings the dada(...) function is now 15-25% faster, and isBimeraDenovo is 2-4x faster.

    o The vectorized Needleman-Wunsch algorithm is now available through nwalign(..., vec=TRUE). This aligner is very fast for short sequences, but performs no overflow checking so use on longer sequences (2kb+) with care.

    o The filenames is now included in the plotQualityProfile plot.

    o The phiX removal functionality in fastqFilter/fastqPairedFilter is now substantially faster.

    o A 2-5% speedup from switching to C++11 hashed containers.

BUG FIXES

    o It is now more difficult to alter the internal structure of dada-class and derep-class objects.

    o assignTaxonomy now works for sequences containg Ns.

    o Bimera detection now correctly handles non-unique sequences in the input.

    o Fixed a memory leak when using the HOMOPOLYMER_GAP_PENALTY option.

    o Fixed the memory leak in isBimeraDenovo and friends.

    o Sequence tables are now integer rather than numeric.

    o Warnings and errors during error estimation from small samples in the dada(…) function are now handled appropriately.

    o Certain diagnostic return values of dada(..., pool=TRUE) are now appropriately constructed.


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