<commit_before>---
title: 'Finch'
tags:
  - minhash
  - Rust
authors:
 - name: <NAME>
   orcid: 0000-0002-8819-9549
   affiliation: 1
 - name: <NAME>
   orcid: 0000-0001-8637-406X
   affiliation: 1
affiliations:
 - name: One Codex
   index: 1
date: 24 August 2017
bibliography: paper.bib
---
# Summary

MinHash [@Broder1997] is a document similarity estimation technique that has been applied to the theoretical bioinformatics problems of sequence search and genome comparisons [@Ondov2016; @Brown2016] and used for testing infectious disease transmission hypotheses [@Sim2017].
We implement two additions to existing minhash schemes: depth tracking of the minhashes and filtering based upon these depths.
Depth tracking allows either rough heuristics on either isolate purity or metagenome complexity.

finch contains a Rust library and a command line tool for creating and manipulating MinHash sketches.

# References<commit_msg>Update paper.md<commit_after>---
title: 'Finch'
tags:
  - minhash
  - Rust
authors:
 - name: <NAME>
   orcid: 0000-0002-8819-9549
   affiliation: 1
 - name: <NAME>
   orcid: 0000-0001-8637-406X
   affiliation: 1
affiliations:
 - name: One Codex
   index: 1
date: 24 August 2017
bibliography: paper.bib
---
# Summary

MinHash [@Broder1997] is a document similarity estimation technique that has been applied to problems in genomics including sequence search, phylogenetic reconstruction [@Ondov2016; @Brown2016], and evaluating outbreaks of hospital acquired infections (HAIs) [@Sim2017].
We implement two additions to existing MinHash schemes: calculating abundances (i.e., minmer counts) during the generation of the MinHash sketches and adaptively correcting for biases introduced due to variable sequencing depth. 
This count information greatly improves the utility of MinHashing when working directly from raw read data (i.e., FASTQ files) and allows more robust estimation of distances between both isolates and complex metagenomic samples. 

`finch-rs` is a Rust library and a corresponding command line tool, `finch`, for creating and manipulating MinHash sketches with abundance information.

# References
{'fraction_non_alphanumeric': 0.06526806526806526, 'fraction_numerical': 0.052214452214452214, 'mean_word_length': 4.603133159268929, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '55633', 'n_tokens_mistral': 692, 'n_tokens_neox': 546, 'n_words': 265}