FOMC 16S rRNA Sequence Analysis Pipeline Version History


2025-05-05 V1.51

Added a section "ALDEx2" for paired sample differential abundance analysis.

2025-05-01 V1.5

Added p values to all alpha- and beta- diversity plots of individual comparisons
Added all levels of taxonomy (from Phylum to Species) for diversity plots and differential abundance analyses
Used MicroViz (https://github.com/david-barnett/microViz) for comparative taxonomy plots


2024-12-01 V1.44
Added several references and did some formating.
Updated reference sequences statistics
Update sequencing platform info

2023-02-26 V1.43
Use ANCOMBC2 instead of ANCOMBC so for pairwise comparison for >= 3 groups

2022-11-17 V1.42
add abundance screenshot and information back

2022-04-12 v1.4 forked
Forked away for FOMC unrelated projects

2022-03-24 V1.41
Fixed a bug in generating the OTU table file "final_otu_table_fullfax_all.txt". Now it is correctly
generated based on final_otu_map_mc100.taxonomy and final_otu_map_mc100.txt

2022-02-04 V1.4

1. Added download for OTU tables with raw count, relative abundance and clr transformed abundance
2. Added heatmaps for 3 clustering options 1) no clustering 2) clustering on species only, 3) clustering on both species and samples

2021-12-17 V1.3

1. Change the comparison to be able to handle group comparison (e.g., not
   only pairwise comparision
2. Added QIIME 2 alpha-group-significance result
3. Added QIIME 2 beta-group-significance result


2021-11-10 V1.2

1. Added this version history to keep track of features added and bugs fixed
2. Added AncomBC differential abundance analsysis
3. Added results for groups in individual comparisons, such as alpha diversity 
   box plots, beta diversity plots, top species/genus/family bar plots, and 
   heatmaps.
4. Changed MC (minimal read count per species) to MPC (minimal percent read
   count per speices) to filter low abundant species by percent abundance of total
   reads. Currently set at MCP=0.1%, so species with fewer than total reads x 0.001
   will be removed for downstream anaalyses.

2021-06-01 V1.1

1. Removed inclusion of the original Zymo absolute abundance plot

2021-03-15 V1.0

1. First version V1.0 released
