SCVUC v4.3.1

This version has been updated to use the VSEARCH --search_exact function instead of --usearch_global --id 1.0 because --search_exact is faster and optimized for finding short exact matches instead doing global alignments.

SCVUC v4.3.0

Update pipeline to translate ESVs then use HMMER profile hidden Markov model sequence analysis to remove bit score outliers (putative pseudogenes) instead of just translating and removing ORF length outliers (v4.2.0).

SCVUC v4.2.0

Streamline the conda environment to remove R packages not needed to run this pipeline. Added GLIBC_2.14 and instructions to set LD_LIBRARY_PATH to point to libc.so.6 needed to run ORFfinder.

SCVUC v4.1.0

Provides a snakemake pipeline to process reads and summarize taxonomic assignments for each ESV in each sample.

Also provides an updated snakemake pipeline that attempts to remove arthropod pseudogenes and produces a report that includes the sequence for the longest retained open reading frame. For pseudogene removal, this version is more sensitive than v4.0.0.

SCVUC v4.0.0

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.

Consolidates several scripts that together parsed nucleotide open reading frame sequences and removed those with outlier lengths (ORFs that are too short or too long) that are putative pseudogenes.

Updates ORFfinder settings to retrieve ORFs for plus strand only, ignoring nested ORFs, minimum length 30bp.

Includes a config file for the COI-ml-jg amplicon.

SCVUC v3.3.2

Update config files, snakefile, and get_longest_orf_nt5.plx so that if multiple ORFs of equal length are found, the first one is consistently retained for further analysis.

SCVUC v3.3.1

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

SCVUC v3.3.0

Fixes a bug leading to an incorrect number of reads in the ESV table that was first introduced with SCVUC v3.
Cleans up summary of statistical output.
Streamlines ORF filtering to remove outliers.
Updates CUTADAPT 2.4 to 2.5
Updates VSEARCH 2.13.6 to 2.14.1

SCVUC v3.2.0

Update stats output files.

SCVUC v3.1.1

Updated the README.