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  • ninja.py: Now automatically detects number of threads to use for aligner (thanks bhillmann!)
  • ninja_parse_filtered: Rewrote parser for low memory use and slightly better I/O performance
  • Databases: Added SILVA v123 ribosomal database
  • Databases: Moved databases to external site, currently http://ni…
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  • New OTU compaction options (now default). Now breaks ties between equally good reference matches deterministically instead of at random (pools all equally good matches into single OTU id). Please consider carefully whether this behavior is desired for your statistical analyses. (Use -K to suppre…
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  • Documentation: Fix outdated instructions for taxonomy sorting, similarity as %, etc
  • ninja.py: New option to enable both forward and reverse strand matching -z (--both_strands)
  • ninja_filter: Removes extraneous carriage returns from input sequence headers
  • ninja_parse: Adds newline to end of otu_map
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  • ninja_prep: now builds databases from a FASTA with string headers, line splits, comments, blank space, etc
  • ninja_prep: removed unnecessary variable region trimming and sorts
  • ninja_prep: now inserts spacers flanking marker genes; disable with --no-spacers
    • spacers allow for better chimera handlin…
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  • Fixed a bug in -m max (wrapper only)
  • New feature: auto-detect whether input fasta has as many samples as sequences; if it does, treat as one sample and warn user
  • New feature: LOG mode in parser now outputs what all matched sequences aligned to (ninja_pass.log). In wrapper, simply use -F to enabl…
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  • Explicit paired-end support (in wrapper; optional distance parameter)
  • Filtered file shows reasons for filtering
  • Alternative ambiguous base handling schemes (discard or convert A)
  • New commandline options and documentation
  • Fix Mac crash in parser in certain situations
  • Streamlined BIOM 1.0 format
  • R…
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  • removed relative paths
  • ninja executable is now in the bin directory
  • cleaned up python code
  • now properly prints errors from spawned subprocesses
  • writes to both stdout and log
  • precompiled linux binary includes static libraries
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  • Much faster support for -F full output mode.
  • Now outputs a list of all IDs of sequences that failed to pass the filter step, and a separate list of all IDs of sequences that failed to match the reference database.
  • Added support for legacy output.