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Mangul-Lab-USC

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This is the GitHub repository for our recent study "Technology dictates algorithms : Recent developments in read alignments." Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

benchmarking_SV

Updated figures for "A benchmarking of WGS-based structural variant callers" paper

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benchmarking_error_correction

This is the GitHub repository for our benchmarking study "Benchmarking of computational error-correction methods for next-generation sequencing".

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pyTCR

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db.microbiome

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Mangul-Lab-USC.github.io

Website for Mangul Lab.

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TAIR

The Atlas of Immunoglobulin Repertoires (TheAIR)

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RNA-seq

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review-technology-dictates-algorithms

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.

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metadata_sepsis

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enhancing_reproducibility

HTML

ImReP_publication_old

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benchmarking-transcriptomics-deconvolution

Paper can be found here : https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab265/6338547

C++

needle

Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome profiling on the strain level.

Shell

biomedical_data_science

TCR-Seq-benchmarking

Comparison of Captured immune repertoire by TCR seq versus imrep, MIXCR, and TRUST4

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TCR-profiling-benchmark

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genomics.USC.HPC

rna.seq.pipeline for USC HPC

Shell

omics-data-reusability

septic.shock.data

ImReP_publication

pyTCR_publication

BioLLMBench

VISTA

Introduction-to-bioinformatics-and-biomedical-data-science

This is a six module graduate-level course covering the fundamentals of transparent and reproducible bioinformatics, targeted towards biomedical students.

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consistency_read_aligners

Python

COVID_bioinformatics

Code and figures for our COVID paper

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Twitter-editorial

Repository has code, figures and paper for twitter editorial.

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sbt

Shell

BWA_Tutorial

A tutorial for generating sequence alignments using BWA

pkg-manager-review

Manubot Repo for Package Manager Review Paper

HTML

omics-packaging-containerizing

This is the GitHub repository for our recent study "Packaging and containerizing of bioinformatics software: advances, challenges, and opportunities" Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.

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annie_project

clonality and cell type composition of patients with persistent bacteremia. Extracted from bulk RNA Seq Data.

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sbt_old

Seeing Beyond the Target (SBT) - computational protocol to process off target reads in WXS experiments

Shell

Mangul-Lab-USC/technology.dictates.algorithms

Mangul-Lab-USC

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