Noah Legall's repositories
dev_script
Cluster scripts and programs
bacteria_SNP
Salvador Lab in-house variant calling script for Sapelo2 (still in development )
sliding-window-scripts
python scripts to analyze multi-sequence alignment (FASTA) data
ANOMA
an R command line tool to find outliers in data unsupervised
Aug-SeptRotation2018
Rotation project based on best practices to study metabolomic data. Wrote python scripts to extract enriched metabolites and do some analysis.
CPPHelloWorld
Code for C++ beginner
EpiModel
Mathematical Modeling of Infectious Disease Dynamics
METRI
Multiomic integration of metagenomic and metatranscriptomic data
MLMessage
Web App Messaging with Machine Learning features built in place
NAST
pairwise BLAST, but with a hint of Noah
pansplit
a command line tool for pangenome creation based on metadata
recombination_heatmap
takes the gubbins GFF output and creates a heatmap csv for further processing
mbovpan_auxilary_files
files that assisted in development of mbovpan, but are not necessarily needed in the main repo
MSA_trim
A tool to trim multi-sequence alignment for gaps and ambiguity codes.
multihostR
Transmission Simulator based on Multi-Host SIR model parameters.
PangenomePipelineScripts
A repository for the scripts I developed to do pangenome inference using SPAdes, prokka, and Roary.
Presentations
All my presentations through the PhD process
Scoary
Pan-genome wide association studies
SNP-Align
take VCF files (preferably filtered) and creates fasta output for SNP positions.
SRA_scraper
A tool to access NCBI SRA Run Selector metadata
SupervisedMotifScanner
Generate a PSSM with sequence test data. non concurrent
TRP-orfamide-interaction
in-silico modeling of TRP28 protein for docking analysis of orfamide A, a toxin of microalgae C. reinhardtii
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
VCF_parser
extract no. of SNP, Insertions, and Deletions
vSNP
vSNP -- bacterial validation SNP analysis tool -- USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. SNP pipeline. Genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.
vSNP_filter
bash script to filter out poor mapping quality SNPs called from vSNP program and PE/PPE genes from analysis.