Coverage graph creator from BAM files (included in the SSV-Conta package)

Mobile Element Insertion Breakpoint Analyzer (MEIBA)

Snakemake pipeline to merge gnomAD VCF files

Coverage graph creator from BAM files (included in the SSV-Conta package)

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

Detection of unknown genetically modified organisms

NGSimulator is a tool to benchmark variant callers. It generates reads simulating sequencing errors such as insertion, deletion, and substitution with variants at user-defined positions.

This program is able to align reads to a database with genomes of reference and support single or paired-end reads from Illumina sequencing technology in FASTQ format (or fastq.gz)

The ChIP-Seq peak calling algorithm using convolution neural networks

Tools for analyzing NGS sequence data and aligned protein sequences

NGS data analysis scripts for HBV elimination research group

Various scripts for working with NGS data in file formats such as VCF, BAM/SAM, and JSON

Exercises and Implementation

RNA-Seq pipeline

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

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, …

Multisample DNAseq variant calling pipeline for use in diagnostics

Protein Analysis and Classifier Toolkit