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Simon Ye (yesimon)

yesimon

Geek Repo

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Location:Cambridge, MA

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Simon Ye's repositories

metax_bakeoff_2019

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dotfiles

Config files for shell

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ART

ART simulator

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Azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

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BEAR

A Better Sequencing Simulator for Metagenomics

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bioconda-recipes

Conda recipes for the bioconda channel.

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bioconda-utils

Utilities for building and managing bioconda recipes

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blastutil

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Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

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cdhit

Automatically exported from code.google.com/p/cdhit

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contra

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diamond

Accelerated BLAST compatible local sequence aligner.

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dx-toolkit

DNAnexus platform client libraries

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gemtools

GEMTools main repository

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kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

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kraken

Kraken taxonomic sequence classification system

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kraken2

The second version of the Kraken taxonomic sequence classification system

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krakenuniq

🐙 Metagenomics classifier with unique k-mer counting for more specific results

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myoaav_capsid

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ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

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ncbitax

NCBI Taxonomy

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pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

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RAPSearch2

Reduced Alphabet based Protein similarity Search

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seaborn

Statistical data visualization using matplotlib

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seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

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snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

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staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

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surpi

SURPI

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viral-ngs

Viral genomics analysis pipelines

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viral-ngs-deploy

Deployment files related to https://github.com/broadinstitute/viral-ngs

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