BIOM fix and addition of script to get num reads in QIIME2 FASTQ files

LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

GNU General Public License v3.0

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Closed gavinmdouglas closed 5 years ago

gavinmdouglas commented 5 years ago

Addressed deprecated issue https://github.com/LangilleLab/microbiome_helper/issues/30 in convert_dada2_out.R: now outputs BIOM file in legacy TSV format to get around issues with biom and biomformat R packages.
Added script qiime2_fastq_lengths.py, which can be used with QIIME2 artifact files to keep track of how many reads were filtered out at various pre-processing steps.