SCVUR v3.0.2

New release to activate Zenodo DOI.

SCVUR v3.0.1

This version of the classifier now uses --search_exact instead of --usearch_global with --id 1.0 to map primer-trimmed reads to denoised ESVs to construct the ESV.table (ESVs x samples). We have made this change because --search_exact is faster and optimized to find exact matches.

SCVUR v3.0.0

Updates the conda environment to myenv.3 .

Uses VSEARCH v2.14.1 to create dereplicate reads, produce denosised ESVs (instead of USEARCH), remove chimeric sequences, and create the ESV x sample table.

SCVUR v2.2.1

Updates the conda environment.yml to use myenv.2 that correctly specifies CUTADAPT v2.6 as well as the snakefile and README files.

SCVUR v2.2.0

Fixes a bug leading to an incorrect number of reads in the ESV table that was first introduced with SCVUR v2.
Cleans up summary of statistical output.
Updates CUTADAPT 2.4 to 2.5
Updates VSEARCH 2.13.6 to 2.14.1

SCVUR v2.1.5

Edited the alternate pipeline to include a manual step where Zotu version numbers are added to the cat.denoised files from each run so that they can be distinguished after combining these files.

SCVUR v2.1.4

Automatically summarize statistics. Add alternate pipeline to process batches of sequencing runs one at a time to stay within 32-bit USEARCH memory limit.

SCVUR v2.1.3

only use a single thread for dereplication step to avoid warning message

SCVUR v2.1.2

removed duplicate config and snakefiles

SCVUR v2.1.1

Corrects the RDP classifier command, does 16S taxonomic assignment by default.

Changes the Perl script that maps read abundance to taxonomic assignments by correcting the names of the column headers.