MetaCache 2.1.1

• More refactoring and code cleanup
• Bug fixes

MetaCache 2.1.0

Improvements

• Enabled longer reads for the GPU version (previous limit was 127 bps)
• Significantly reduced number of temporary allocations on host
• Some more refactoring and code cleanup

Fixes

• Skip empty lines in input files
• Fixed conversion warning

MetaCache 2.0.1

• Fixed wrong load factor in query mode resulting in high load times (#22)

MetaCache 2.0.0

New: MetaCache-GPU

• building and querying on CUDA-capable accelerators
• multi-GPU support for distributing and/or replicating databases across multiple GPUs
• ultra-fast database building: ~10 seconds for the complete Refseq 202 (bacteria+viruses+archaea) on 4 NVIDIA(R) Tesla(R) V100 GPUs
• faster querying: ~300 million reads per minute for a Refseq 202 database on 4 NVIDIA(R) Tesla(R) V100 GPUs
• GPU-built databases can be used with the CPU version and vice versa (needs to be partitioned so that each part fits in GPU memory)
• MetaCache-GPU will be presented at ICPP '21

Further Improvements

• support for reading gzipped FASTA/FASTQ files (requires zlib to be installed, see installation instructions)
• mode "build+query" for building and directly querying a database (great for the GPU version)
• improved CPU querying speed
• new database format (incompatible with previous versions of MetaCache)
• improved database reading/writing performance
• more useful progress indicators

MetaCache v1.1.1

• fixed critical bug that lead to increased memory consumption during database build
• control characters like \t are now properly handled in the -separator option
• fixed g++5 compilation bug
• fixed some smaller bugs
• improved the documentation explaining the output analysis and display options
• more consistent progress bar display across different operations
• some code reorganization

MetaCache v1.0.0

• re-written command line interface with proper diagnostics; there shouldn’t be any breaking changes (regarding option names, etc.)
• updated and improved documentation
• removed hardly used and brittle "annotate" mode that was out of the scope of MetaCache anyway
• small performance improvements
• some minor bug fixes

MetaCache v0.9.0

• improved query speed, especially better thread scaling beyond 32 threads (ca. 50% faster with 88 threads)
• improved database loading speed
• database loading indicator
• small bug fixes
• improved code structure

Attention:

You need to rebuild your databases for this version, because it uses a new database binary format. Disk and RAM consumption are not affected.

MetaCache v0.8.0

New feature "Coverage Filter"

Option -cov-percentile <p> removes the p-th percentile of hit targets (reference genomes) with the lowest coverage. A first pass does the normal mapping of queries (reads) to targets (reference genomes). The actual classification is then done in a second pass using only the remaining hit targets.

This will lead to a very small increase in runtime and memory consumption but can improve accuracy by detecting and removing stray false positive hits.

The coverage filter is deactivated by default.

Other Changes

• improved multi-threading in query mode
• improved database format (layout better suited for future loading on GPUs)
• code cleanup

MetaCache v0.6.2

• improved accession number / sequence id parsing
• file reading improvements
• code cleanup

MetaCache v0.6.1

• improved database building performance (~30-50% speedup)
• improved taxonomic id assignment during build: now one can also use global assembly_summary files
  (default: "assembly_summary_refseq.txt", "assembly_summary_refseq_historical.txt", "assembly_summary_genbank.txt", "assembly_summary_genbank_historical.txt" in the taxonomy folder)
• the download-ncbi-taxonomy script downloads "assembly_summary_refseq.txt" and "assembly_summary_refseq_historical.txt" by default now
• code cleanup