Jackson M. Tsuji's repositories
metannotate-analysis
Code to process and visualize output from MetAnnotate (DoxeyLab tool)
atlas-extensions
Extensions to the PNNL ATLAS pipeline
PANDAseq-MGtools
Collection of scripts to optimize and use PANDAseq for paired-end alignment of metagenomic reads
96-well-spec-analysis
Scripts for quickly processing 96 well plate data from the Neufeld lab spec
axiome-extensions
Misc personal scripts to extend or improve AXIOME
chlorobia-cyc2-genomics
Companion repository to the manuscript, "Anoxygenic photosynthesis and iron–sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes"
GC-spec-analysis
A collection of scripts for working with GC/spectrophotometer data. Includes converting from standard curves, and so on.
atlas-wrapper
A wrapper to run ATLAS within a Docker container
atlas2-helpers
Helper scripts for post-processing of ATLAS output, version 2 and higher
basic-sequence-analysis
Personal scripts for performing basic sequence file manipulations (FastA, FastQ)
Ca-Chlorohelix-allophototropha-RCI
Code repository associated with the manuscript, "'Candidatus Chlorohelix allophototropha,' the first anoxygenic phototrophic Chloroflexota member to use a Type I photosynthetic reaction center"
qiime2-helpers
Helper scripts to streamline QIIME2 analyses
bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics-m1
Notes about migration to an M1 Mac as a bioinformatics user
jmtsuji.github.io
Back end of research intro website
tellread_format_conversion
Simple scripts for handling the output of the TELL-Read pipeline