mapseq v2.1.1 - reference 3.0

v2.1.1 update:

• Added paired end analysis for FASTQ. The previous version (v2.1) only supported FASTA sequence data.

v2.1 update:

• Updated MAPref to v3.0 with new MAP OTU labels as used on the Microbe Atlas Project website (https://microbeatlas.org/)
• Updated NCBI taxonomy (Feb 2021)
• Added paired end analysis which automatically handles overlapping and non-overlapping paired end sequence mapping
• Added a sensitive mode (-sens) for more accurate analysis needed in some applications
• Added -asvotutable option to generate a merged count table with MAP OTU labels or NCBI taxonomy using as input one or more ASV count tables that may cover different 16S regions

mapseq v2.1 with updated reference 3.0

• Updated MAPref to v3.0 with new MAP OTU labels as used on the Microbe Atlas Project website (https://microbeatlas.org/)
• Updated NCBI taxonomy (Feb 2021)
• Added paired end analysis which automatically handles overlapping and non-overlapping paired end sequence mapping
• Added a sensitive mode for more accurate analysis needed in some applications
• Added -asvotutable option to generate a merged count table from several ASV count tables

Bug fix in -otutables option

Fixed a bug in -otutables that populated the table with counts only from the first sample provided.

mapseq-1.2.6-macosx.tar.gz - statically compiled binary on MacOSX (Mojave 10.14.6)
mapseq-1.2.6-linux.tar.gz - statically compiled binary on a linux kernel v4.15 (ubuntu 18.04)
mapseq-1.2.6-linux.kernel3.13.tar.gz - statically compiled binary on linux kernel 3.13 (ubuntu 14.04)

v2.0alpha pre-release with experimental paired end sequence mapping

Pre-release of version 2.0 with experimental paired end sequence mapping.

Paired end sequencing can be mapped using the "-paired" option:
mapseq -paired pairend1.fna pairend2.fna

MAPseq will use both pair ends in the search and alignment to identify the taxonomy of the paired end reads. Both overlapping and non-overlapping paired ends are handled by mapseq automatically.

v1.2.5 - OTU counts and table generation from mseq files

New features:

• Added "-otucounts" and "-otutable" options to generate count summary for single mapseq (.mseq) files or an otu/taxa table for multiple .mseq files
• Added "-ignoreEmptyTax" option. Default is off until thorough benchmarks are performed.
  Prevents second hits with missing taxonomic labels (uncertain annotation) from decreasing the confidence of the top hit assignment.

mapseq-1.2.5-macosx.tar.gz - statically compiled binary on MacOSX (Mojave 10.14.6)
mapseq-1.2.5-linux.tar.gz - statically compiled binary on a linux kernel v4.15 (ubuntu 18.04)
mapseq-1.2.5-linux.kernel3.13.tar.gz - statically compiled binary on linux kernel 3.13 (ubuntu 14.04)

Bug fixes and update to MAPref2.2b

Bug fixes:
Fixed missing newline causing last sequence to be missed, added assert on empty sequences
Fixed double hits reported when classifying long queries (>1200bp)

Updated to mapref-2.2b:
Removed low quality reference sequences that would cause issues when classifying low quality query sequences.

mapseq-1.2.3-macosx.tar.gz - statically compiled binary on MacOSX (Sierra)
mapseq-1.2.3-linux.tar.gz - statically compiled binary on a linux kernel v4.15 (ubuntu 18.04)
mapseq-1.2.3-linux.kernel3.13.tar.gz - statically compiled binary on linux kernel 3.13 (ubuntu 14.04)

update to MAPref v2.2

Updated reference to MAPref v2.2:

• fixed multithreaded race condition affecting occurring on some machines
• v2.0 had an over-proportional increase in number of OTUs compared to v1.0 due to changes introduced in the alignment and trim settings. This has now been rectified and the increase is more inline with expectations.
• Several sequences in v1.0 were missing in v2.0 and are now included in the new version.

linux binaries - updated mapseq reference 2.0

The reference was updated to include many more sequences (now 1.5 million compared to almost 1 million in the previous version). Mitochondrial sequences that were not aligned to the 16S and 18S models used with infernal were now included in this version if they were found to be annotated as such in the NCBI RefSeq database. Mitochondrial 16S coverage should therefore be much improved in this release.