CHANGES IN VERSION 1.3.5 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o The default chimera removal method is now "consensus" in the removeBimeraDenovo function (method="consensus"). o The filtering functions now remove phiX by default (rm.phix=TRUE). CHANGES IN VERSION 1.3.4 ----------------------- NEW FEATURES o filterAndTrim is the new multithreaded interface for filtering and trimming. It is R-vectorized, in that it accepts vectors of input/output files. Supports both single-read and paired-read filtering. SIGNIFICANT USER-VISIBLE CHANGES o Consensus chimera removal now supports multithreading. o The new trimOverhang option in mergePairs allows the portion of paired reads that overhang the start of the other read to be removed when merging. o Faster filtering by not enforcing redundant filtering conditions. CHANGES IN VERSION 1.3.3 ----------------------- NEW FEATURES o ITS support. The dada method now handles variable-length amplicons, which allows common ITS sequencing strategies to be processed. Taxonomic assignment against the UNITE database is also now available. SIGNIFICANT USER-VISIBLE CHANGES o The xxxFilter methods now have maxLen and minLen filtering parameters. CHANGES IN VERSION 1.3.2 ----------------------- NEW FEATURES o learnErrors is a new method for learning error rates from a targeted number of reads. This wraps pre-existing functionality -- dada(..., selfConsist=TRUE) -- in a much easier to use form. o assignTaxonomy is multithreaded (multithread=TRUE) and can individually test reverse-complemented sequences and use them to classify if they better match the reference (tryRC=TRUE). CHANGES IN VERSION 1.3.1 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o The xxxFilter methods now (invisibily) return the number of reads that went in and that passed the filter. o fastqFilter now has a maxLen parameter, primarily for filtering/trimming 454 data. BUG FIXES o trimLeft is now enforced before any filtering is performed. o Rscript invocations should now work without requiring an initial library(methods) call. CHANGES IN VERSION 1.1.7 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o The isBimeraDenovoTable method is now available through the convenience interface removeBimeraDenovo(..., tableMethod="consensus"). 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. BUG FIXES o It is now more difficult to mess up the internal structure of dada-class and derep-class objects. CHANGES IN VERSION 1.1.6 ----------------------- NEW FEATURES o isBimeraDenovoTable is a new function for detecting chimeras on multi-sample sequence tables. It first identifies bimeras on a per-sample basis, and then uses a consensus approach to identify bimeric sequences. This improves the specificity of bimera classification for datasets with many samples. SIGNIFICANT USER-VISIBLE CHANGES o The filenames is now included in the plotQualityProfile plot. BUG FIXES 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 Warnings and errors during error estimation from small samples in the dada(…) function are now handled appropriately. CHANGES IN VERSION 1.1.4 ----------------------- NEW FEATURES o Multithreaded chimera detection. The isBimeraDenovo(...) function is now multithreaded. This behavior is controlled by the multithread argument to the function, and is FALSE by default. CHANGES IN VERSION 1.1.3 ----------------------- 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. CHANGES IN VERSION 1.1.2 ----------------------- NEW FEATURES o Species-level taxonomic assignment. The new assignSpecies(...) function uses exact matching to assign sequences to the species level. Currently a valid species training fasta is only available for the RDP taxonomic database. CHANGES IN VERSION 1.1.1 ----------------------- BUG FIXES o Fixed the memory leak in isBimeraDenovo and friends. o Sequence tables are now integer rather than numeric. CHANGES IN VERSION 1.1 ----------------------- 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. SIGNIFICANT USER-VISIBLE CHANGES o The phiX removal functionality in fastqFilter/fastqPairedFilter is now substantially faster. BUG FIXES o Certain diagnostic return values of dada(..., pool=TRUE) are now appropriately constructed. o A 2-5% speedup from switching to C++11 hashed containers. 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