Stephane Plaisance's repositories
NGS-Variant-Analysis-and-coverage-depth
Subsample a large Drosophila dataset to measure the effect of coverage depth on variant calls
venn-tools
R scripts to plot Venn diagrams for 2,3,4-way Venn from counts
comparing_NGS-mappers
code for a white paper on our WIki
NGS-Variant-Analysis-training-2016
Adapted session for a one-day training
qiime-tools
scripts and methods to use Qiime2 on long-reads
Summer_school_2018
Exchange platform for sharing issues and advice during the training
DevNet
The DevNet project on github stores the PacBio DevNet website.
flo
Same species annotation lift over pipeline.
fork-repository
This repository is made for teaching purposes.
GenomicConsensus
PacBio® variant and consensus caller
github-slideshow
A robot powered training repository :robot:
lotus2
Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
markdown-cheatsheet
Markdown Cheatsheet for Github Readme.md
mockcommunity
Long-read mock community experiments
NGS-Variant-Analysis-training-2020
Adapted training for GATK 4.1.4.x
phased_primers_shiny
Shiny app to create phased PCR 1 primers for amplicon library preparation.
plotting-tools
code to plot from numbers
q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
read2tree
a tool for inferring species tree from sequencing reads
text-tools
Parsing and filtering delimited text data
TIDDIT
TIDDIT - structural variant calling
wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly