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darlenes_data

darlenes_data_mining

Scripts which perform web scraping, spreadsheet parsing, or both

dataviz_for_fastq

A showcase of functions using Biopython, including FastqGeneralIterator, along with pandas and matplotlib for teaching Big Data parsing for NGS

fixnextflowsamplesheet

howdy

Howdy

nextflowtrimviral

nextflowviral

Pipelines written in Nextflow and Python to facilitate comparative genomics analysis for viruses. Requires Python 3.9.1 or above and Nextflow 21.04.3 and above.

ngs_multi_heal

NGS_Multi_Heal simplifies quality analysis, trimming, and healing of paired-end reads

ngs_plot_widgets

Provides graphical and .json output for paired-end Next-Generation Sequencing (NGS) data as well as genome coverage data from .bed files. Requires Python 3.9.1 or higher.

ngs_qc_piper

Automates Illumina paired-end fastq NGS sequencing quality assurance.

parse_blast_python

python scripts for reading blastn output and manipulating text files for blast databases

rdase_curator

A retrieval, annotation, curation tool for cofactor-dependent core metabolic proteins

seq_fetch

Wrapper scripts for NCBI sratoolkit. Retrieves NGS data as Sequence Read Archive (SRA) from NCBI.

snp_wrap_python

Facilitates post-processing of SNP pipeline outputs

text_munge_pl

Command-line perl scripts to automate routine, boring text editing tasks, such as formatting author's lists for EndNote