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argoworkflowgenerator

Java based workflow generator to deploy WES variant detection pipelines on Kubernetes using Argo. Reads WDL files and produces Argo compatible work flows specifciying compute cluster environment (pod) on which the workflow component should be executed and the buckets in which the results should be dropped

backpropagationneuralnetwork

backtranslationproteintoputativedna

Gives most probable and least probable DNA Sequences for input protein sequence

baselinesurveyresponsesimulator

Simulation of baseline survey response variables to store information in EPIC Number of variables: 495 Code: Java 8 Reads in csv file of variables and value range of permitted responses Use randomization to a) induce error b) generate valid responses, and simulate 1M responses, to use as prototype data to populate i2b2 deployments in support of the MVP project for VABHS

cabio-load-scripts

ETL scripts to populate caBIO database

calculatecodonfrequency

perl script that reads file in multifasta format and complements it

camodloadscripts

ETL scripts to populate caMOD database with MTB data from Jackson Labs

dnaextractionmodule

Code that polls beckman coulter and stores rack information, and protocols initiated (if any) on samples.

dnatoproteintranslation

Converts DNA to Protein along 1, 6 (fwd or reverse strand) or user defined frames

elegant-scipy

1st Edition of Elegant SciPy (O'Reilly Publishers)

fastqcparser

Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific position in a read alignment against the reference genome), per base seq quality (across aligned reads), per base sequence content, per base quality scores, per tile sequence quality

findnmerfrequencies

C++ code to calculate nmer frequencies (n= 1 to 6) and write out to file

findpalindromesandinvertedrepeats

Finds palindromes and inverted repeats in DNA Sequences based on user defined inputs

freezerworksinterfacemodule

Interface to Biomek that performs 1D and 2D Scan of aliquots (2d) and rack (1d) ; reads freezer configuration from DB and assigns location to plate

gatkparser

Python package to parse GATK Output and extract summary statistics at mbq 0,10,20,30 and variant evaluation metrics

geneabundance

genemark

interferenceestimation

Java based implementation of an MLE method using chi square test to calculate interference during meiotic crossover (the number of double strand dna breaks that don't result in a crossover)

kmercounter

Kmer counter is written in GO Lang v 1.16.5 To install GO on Windows, follow the instructions at https://golang.org/doc/install 4 GO implementation of N-mer counter in DNA sequences which tests for validity of input. It reads in file name (of fasta file) It reads the size length (kmer length) for which counts are desired and writes out to file, counts of all overlapping kmers of size 1 through the specified input. It checks if fasta file is empty amd whether kmer length is specified.

laminarflowhoodmodule

Module for tracking tubes and aliquots and assign storage in the freezers ; Part of the MVP specimen processing system VABHS. Prototype

microarray

Microarray data analysis using R / BioConductor

naivevariantcaller_ecgr_variantdetection

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

oreillyelegantscipy

paralogidentification

Wrapper script that calls formatdb on nr database and then runs blastall against formatted db and parses the output.

phycastats

16sRNA Microbial Profiling R scripts to find most significant OTUs in 16RNA data after data normalization, followed by ordination and clustering and then plotting iTOL

picardparser

pileupnotationvariantcaller

Variant caller from pileup notation / samtools alignment

primerdesign

probedesign

Takes as input FNA file, PTT file, desired probe length, cross-reactivity allowed, overhang

rebase-using-kmp

restriction enzyme cleavage site identifier using kmp algorithm and REBASE