SyFi - Archived code and test dataset

This Zenodo repository contains the archived SyFi code from the SyFi github (https://github.com/adriangeerre/SyFi). SyFi builds marker sequence fingerprints for bacterial isolates using their genomic sequences and genomic read files. These marker sequences can be employed for SynCom member quantification in large complex SynCom datasets. 

Included in this repository is a small dataset that allows the testing of SyFi, whether installing and running it functions properly. Included in the archive is a readme file with the commands that are to be run, a 16S rRNA sequence fasta file to use as the subject in the SyFi main alignment step, a folder with the bacterial genomic data of eight SynCom isolates according to the SyFi main required folder structure, and a folder with microbiome amplicon data of four samples according to the SyFi quant required folder structure.

Mind that this small test dataset is a subset from the validation dataset of the manuscript, which means that the amount of pseudoaligned reads in the SyFi quant will appear low (only 8 SynCom members of the 447 are included for generating the SyFi fingerprints).