Unexpected cell phone (pre-release)

Mostly quality of life updates:

• anemone detects if barcodes file has empty lines at end of file
• pipeline detects unexpected variable names in conf.py file
• introduced "compress" variable for gzipping at each step
• reduced R package dependencies to "ggplot2" and its prerequisites only

Silent anticipation (pre-release)

Updates to porifera adapter removal tool now require 'adapters.R1.txt' and 'adapters.R2.txt'. When called from the ngsComposer pipeline, porifera utilized the barcodes naming matrix to search only for those adapters that contain barcodes leading to the given sample. If no barcodes are detected, all listed adapters will be considered.

Tapping the baton (pre-release)

Pipeline restructuring and new tool features:

• adapter trimming (porifera) now precedes quality-filtering
• end-trimming is performed using a sliding window (no longer using quartile mode)
• empty directories automatically removed at end of pipeline (unless specified, keeps all qc results)
• crinoid read-count issue (as displayed on figure) corrected
• estimated directory space usage updated

Warm-up (pre-release)

First round of bug fixes and updates:

• implemented new algorithm for adapter removal in porifera
• fixed reads miscalculation in "summary" qc and nucleotide visualizations
• reverted to r1 argument naming scheme for standalone tools
• corrected user input for auto-detection of paired-end reads

Tuning (pre-release)

Please use ngsComposer at your own discretion. Currently, the software is in an early testing release. If you find issues or have suggestions to improve ngsComposer or its documentation, please contact [email protected] or [email protected].