jiarong
Microbial ecologist, bioinformatician, @dib-lab minion, @rdpstaff, @carpentries enthusiast
East Lansing, MI
Pinned Repositories
2014-ssu-search
2015-01-27-msu_icer
Software Carpentry Bootcamp held at Michigan State University on January 27th to 29th, 2015
2021-08-viral-identification-benchmark-review
blog
my blog posts
EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
khmer
in-memory k-mer counting
SSUsearch
A pipeline for extracting SSU rRNA gene from wgs data and applying them for further diversity analysis
stitch
Creates contigs from overlapping, paired-end Illumina reads.
uniqprimer
pipeline to find unique primer for genome bins in metagenomes
VirSorter2
customizable pipeline to identify viral sequences from (meta)genomic data
jiarong's Repositories
jiarong/VirSorter2
customizable pipeline to identify viral sequences from (meta)genomic data
jiarong/SSUsearch
A pipeline for extracting SSU rRNA gene from wgs data and applying them for further diversity analysis
jiarong/uniqprimer
pipeline to find unique primer for genome bins in metagenomes
jiarong/2021-08-viral-identification-benchmark-review
jiarong/2015-11-05-ND
jiarong/2015-glbrc
jiarong/2016-dissertation
jiarong/2016-rplB
jiarong/atlas
ATLAS - Three commands to start analysing your metagenome data
jiarong/aviary
A hybrid assembly and MAG recovery pipeline (and more!)
jiarong/bioconda-recipes
Conda recipes for the bioconda channel.
jiarong/gtdb-taxon-mapping-between-versions
jiarong/jiarong-helloworld
kbase tutorial
jiarong/macsyfinder
jiarong/metapop
A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
jiarong/molevolworkshop.github.io
Future web site for the Workshop on Molecular Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts.
jiarong/MyContigFilter
jiarong/MyContigFilter_gjr
jiarong/protocols
NGS data analysis protocols
jiarong/pydirseq
pydirseq provides gene-wise coverage for metaT and metaG reads mapped to genomes/contigs
jiarong/R-genomics
jiarong/rplB-metaG-pipeline
rplB/rpsC targeted analyses with shotgun metagenomes
jiarong/sampleproject
A sample project that exists for PyPUG's "Tutorial on Packaging and Distributing Projects"
jiarong/SAT-Assembler
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data)
jiarong/seqdep
a tool for estimating sequencing depth of shotgun sequences
jiarong/small-dataset
small datasets for easy sharing
jiarong/viral-ngs
Viral genomics analysis pipelines
jiarong/VirSorter2-SOP
jiarong/vs2-cyverse-app
Scripts for building VirSorter2 Cyverse App
jiarong/xander-assembly-pipeline
xander assembly pipeline to generate OTU and taxonomy table