tourmaline

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Development branch is here: https://github.com/aomlomics/tourmaline/tree/develop Planning doc for Tourmaline 2.0 is here: https://docs.google.com/document/d/1A7rriQ-hwhYD5ZguarRtQAKJDl_MvyfUCa0e00mSxSs/edit @ksilnoaa

lukenoaa

Update fastqc_per_base_sequence_quality_dropoff.py

2

Update [fastqc_per_base_sequence_quality_dropoff.py](https://github.com/aomlomics/tourmaline/blob/develop/scripts/fastqc_per_base_sequence_quality_dropoff.py) to work with fastq_summary.qzv output

ksilnoaa

- Trimming stats - \# of reads per sample - Sequence quality dropoff

ksilnoaa

Have a script that will take non-demultiplexed fastq files and demultiplex them by sample barcodes and/or marker (e.g., from a big NextSeq run).

ksilnoaa

Create table of number of reads retained per sample at each step

3

DADA2 in R provides this and it's very convenient to see what each step is doing

lukenoaa

Tourmaline initial set-up in v2

1

Instead of cloning the github directory every time to start a brand new Tourmaline run, have a Bash script that will generate all of the required input config files.

ksilnoaa

If user is running Rosetta (to enable QIIME 2 to run on Apple Silicon Macs), the instructions to install multiqc conda environment will not work. User first needs to create...

lukenoaa

Test Jupyter notebooks with current Tourmaline notebook, updated package commands

1

ksilnoaa

ksilnoaa

- Option to remove samples with a file and/or below a certain read depth - Option to filter ASVs by length, minimum frequency - Is there a way to cache...

ksilnoaa