Merge pull request #1 from Arcadia-Science/make_metadata

Outline the purpose of the repository and generate project metadata

README.md

@@ -1 +1,19 @@
-# 2022-mtx-not-in-mgx-pairs
+# Identifying sequences that are in a metatranscriptome but not in a metagenome
+
+This repository curates a set of paired metagenomes and metatranscriptomes and provides a pipeline to rapidly identify the fraction of sequences in a metatranscriptome that are not in a metagenome.
+The pipeline is shaped around a metadata file, 'inputs/metadata-paired-mgx-mtx.tsv', that contains a sample name (`sample_name`), metagenome SRA run accession (`mgx_run_accession`; `SRR*`, `ERR*`, `DRR*`), metatranscriptome SRA run accession (`mtx_run_accession`), and a sample type (`sample_type`).
+Using the run accessions, it downloads the sequencing data from the SRA and generates a [FracMinHash sketch](https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2.abstract) of each run.
+Then, it uses the paired information encoded in the metadata table to subtract the metagenome sketch from the metatranscriptome sketch.
+This produces an estimate of the fraction metatranscriptome sequences not found in the paired metagenome.
+These estimates are also clustered by `sample_type` to generate biome-specific estimates.
+The pipeline also analyzes the fraction of metatranscriptome-specific sequences that are shared between samples to discover what fraction of sequences we are systematically missing within and across biomes.
+
+Some metagenome and metatranscripome pairs are true pairs that were extracted from the same sample while others are from separate samples taken from the same location at the same time.
+
+## Getting started with this repository
+
+TBD
+
+## Next steps
+
+TBD