FIX: Several improvements in IonHammer.
FIX: Fixed a few minor bugs in repeat resolution and scaffolding.
NEW: Mate-pair only assembly with high-quality libraties.
NEW: Support for BAM files.
CHANGE: Improved IonTorrent pipeline.
CHANGE: Better quality and higher performance when using mate-pairs.
FIX: Fixed dipSPAdes bugs and user interface.
NEW: Module for assemblying diplod highly polymorphic genomes.
NEW: Support for PacBio reads.
NEW: Support for IonTorrent reads.
NEW: Support for Sanger reads and additional contigs.
NEW: Possibility to restart SPAdes starting from the specified check-point with the
NEW: Output contigs/scaffolds in FASTA and FASTG.
CHANGE: Improved algorithm for mate-pair repeat resolution and scaffolding.
CHANGE: Improved N50 and misassembly rate for single-cell data sets with low genome fraction.
FIX: User-friendly handling for errors in mismatch corrector.
REMOVE: Rectangle graph repeat resolution module.
NEW: Python 3.2 and 3.3 compatibility.
NEW: Possibility to continue SPAdes run starting from the last check-point with the
CHANGE: Decreased memory consumption for error correction module.
CHANGE: Improved misassembly rate for single-cell data sets with low genome fraction.
FIX: User-friendly handling for the case when paired reads do not align to the assembly graph.
NEW: Multiple paired-end and mate-pair libraries.
NEW: Recipe for assembling Illumina 2x150bp and 2x250bp reads.
CHANGE: Improved mismatch and indel rate.
NEW: Mismatch correction post-processing module.
NEW: Rectangle graph repeat resolution module as an option.
NEW: Build for Mac OS.
CHANGE: Improved assembly quality of standard (isolate) data sets.
CHANGE: Decreased memory consumption in error correction module (14 Gb instead of 24 Gb on E.coli test dataset).
REMOVE: SAM-file generation.
NEW: Generate scaffolds alongside with contigs.
CHANGE: Use N instead of A, C, G, T for the variations in repeats.
CHANGE: Memory requirements for E.coli test dataset decreased from 35 Gb to 24 Gb of RAM.
CHANGE: output_dir is a required command line parameter instead of project_name.
CHANGE: Simplified output directory structure.
CHANGE: CMake 2.8 is required instead of 2.6.
REMOVE: No dependency from boost library.
Verification of expression 'v1 == conjugate(v2)' failed error.
NEW: No special binaries for different K values.
NEW: Great improvements in error correction tool BayesHammer.
CHANGE: Memory requirements for E.coli test dataset decreased from 85 Gb to 35 Gb of RAM.
CHANGE: Only 1 iteration of BayesHammer by default.
NEW: Improved assembly quality.
NEW: Support multi-threading.
NEW: Improved algorithms.
NEW: Command-line interface.
CHANGE: Quality assesment separated from the core pipeline.
REMOVE: No support for debian and RPM packages.
FIX: Quality tool fixed.