khmer v2.1 release notes

We are pleased to announce release version 2.1 of khmer! This release includes several new features, bug fixes, and internal changes. CHANGELOG.md includes a complete description of changes made since the previous release. A concise summary of the most relevant changes is provided below.

The latest version of the khmer documentation is available at https://khmer.readthedocs.org/en/v2.1/.

Items of note

New features

• New storage class using half a byte per entry. Exposed as SmallCounttable and SmallCountgraph.
• New Counttable, SmallCounttable, and Nodetable classes to support non-reversible hashing functionality and k > 32.
• Support for human-friendly memory requests (2G) in addition to the previous style of requests (2000000000 or 2e9).
• Support for variable-coverage trimming in the filter-abund-single.py script.
• khmer package version now included in .info files.
• Several simple examples of the Python API and the C++ API in examples/python-api and examples/c++-api, respectively.
• Support for assembling directly from k-mer graphs, and a new JunctionCountAssembler class.
• New sandbox script extract-compact-dbg.py for computing a compact de Bruijn graph from sequence data.

Bug fixes

• Streaming gzip-compressed output from scripts now works correctly.
• The load-graph.py script now calculates required graph space correctly.
• The broken_paired_reader no longer drops short reads when require_paired is set.

Other changes

• Command-line options -x and -N now suppressed by default in script help messages.
• Renamed core data structures: CountingHash --> Countgraph, Hashbits --> Nodegraph.
• Replaced the IParser and FastxParser classes with a single ReadParser class. Different input formats are supported by templating ReadParser with a reader class.
• Renamed consume_fasta and related functions to consume_seqfile, with support for reading sequences from additional formats pending.

Known issues:

• load-graph.py in multithreaded mode will find slightly different number of unique kmers. This is being investigated in https://github.com/dib-lab/khmer/issues/1248
• Any scripts that consume FASTA or FASTQ data are unresponsive to attempts to terminate the program with ctrl-c. Eventually khmer should handle this properly, but for now it should be possible to halt a script using ctrl-\. This is being tracked in https://github.com/dib-lab/khmer/issues/1618.

Contributors

‡@aaliyari, @ctb, ‡@caitsydney, @camillescott, @standage, @kdmurray91, @ljcohen, @luizirber, @mr-c, ‡@NBKingsley, ‡@ryneches, ‡@rcs333, ‡@satta, ‡@shannonekj, ‡@betatim

‡ Indicates new contributors

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