scPathoQuant testSets

This repository contains all codes for testing software scPathoQuant which can be download from here

HIV test set (Bradley_et_al_testSet/)

Data to test scPathoQuant used from the following paper Bradley T, Ferrari G, Haynes BF, Margolis DM, Browne EP. Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency. Cell Rep. 2018 Oct 2;25(1):107-117.e3. doi: 10.1016/j.celrep.2018.09.020. PMID: 30282021; PMCID: PMC6258175.

Codes are run in the order of which they are numbered

1.DownloadData.sh - Download raw data from SRA website
2a.SCprocessinghg38_HIV_sb.sh - align raw data to human genome with HIV genome integrated
2b.SCprocessinghg38_sb.sh - align raw to human genome only
3.scPathoQuant.sh - align results from 2b to HIV genome
4.SC_Analysis.r - run analysis on data generated from scPathoQuant (results for scPathoQuant paper)
genomefiles/ - contains HIV genome files

Sars-Cov2 test set (Ravindra_et_al_testSet/)

Data to test scPathoQuant used from the following paper Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biol. 2021 Mar 17;19(3):e3001143. doi: 10.1371/journal.pbio.3001143. PMID: 33730024; PMCID: PMC8007021.

Codes are run in the order of which they are numbered

1.DownloadData.sh - Download raw data from SRA website
2a.CellRanger_Sars-CoV2_sb.sh - align raw data to human genome with HIV genome integrated
2b.CellRanger_sb.sh - align raw to human genome only
3.scPathoQuant.sh - align results from 2b to HIV genome
4.SC_Analysis.r - run analysis on data generated from scPathoQuant (results for scPathoQuant paper)
genomefiles/ - contains sars-cov2 genome files

Co-infection of Sars-Cov-2 and Metapnemonivirus (Rosin_et_al_testSet/)

Data to test scPathoQuants ability to quantify multiple infections in a single cell sample. We use data set from Rosin NL, Jaffer A, Sinha S, Mulloy RP, Robinson C, Labit E, et al. SARS-CoV-2 Infection of Circulating Immune Cells is Not Responsible for Virus Dissemination in Severe COVID-19 Patients. Rochester, NY; 2021. Available from: https://papers.ssrn.com/abstract=3771665 to replicate co-infection first identified by 'ViralTrack with scPathoQuant.

Codes are run in the order of which they are numbered:

1.DownloadData.sh - code to download necessary data
2.CellangerWithSPQ.sh - code to run CellRanger with scPathoQuant
genomefiles/ - contains sars-cov2 and metapnemovirus genomes

Benchmarking scPathoQuant against other tools

Here we provide codes used for benchmarking scPathoQuant against 'ViralTrack, Venus and PathogenTrack

CellRangerwithSPQBench.sh - commands to run scPathoQuant
PathogenTrackBench.sh - commands required to run PathogenTrack
VenusBench.sh - commands required to run Venus
ViralTrackBench.sh - commands required to run ViralTrack

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