Update README.md

README.md

@@ -4,3 +4,37 @@ Detect HIV Drug Resitant Mutations using amplicon sequencing data
 A production-ready re-implementation of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7699007/,
 https://github.com/Wei-Shao/HIV-DRLink.
 
+## How to run
+
+```bash
+hivdrm.py --barcodes barcodes.csv --reference reference.edited.fasta r1.fq.gz r2.fq.gz
+```
+
+Example of barcodes.csv:
+```
+Sample_ID,Primers,F-Linkers,R-Linkers
+S01,F1/R1,CGCCTG,GCCATG
+S02,F1/R2,CGCCTG,TACAAG
+S03,F1/R3,CGCCTG,ATTCCG
+S04,F1/R4,CGCCTG,TCGGGA
+S05,F1/R5,CGCCTG,GAATGA
+S06,F1/R6,CGCCTG,GCCTAA
+S07,F2/R1,CGTGAT,GCCATG
+S08,F2/R2,CGTGAT,TACAAG
+S09,F2/R3,CGTGAT,ATTCCG
+S10,F2/R4,CGTGAT,TCGGGA
+S11,F2/R5,CGTGAT,GAATGA
+S12,F2/R6,CGTGAT,GCCTAA
+S13,F3/R1,CTGATC,GCCATG
+```
+
+Example of reference.fasta:
+```
+>EF602219.1 HIV-1 isolate 1779 from South Africa pol protein (pol) gene, partial cds edited
+CGCCTGAATCCATATAACACTCCAATATTTGCCATAAAAAAGAAGGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGGGAACTTAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACATCCAGCAGGATTAAAAAAGAAAAAATCAGTGACAGTACTGGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGATGAAGGCTTCAGAAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCAGGGATTAGATATCAATATAATGTGCTCCCAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAGAAATCCAGAAATAGTCATCTATCAATATATGGATGACTTGTATGTGGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAGGAATTAAGAGCACATTTATTAGGGTGGGGATTTACCACWCCAGACAAGAAACATCAGAAGGAACCCCCATTTCTTTGGATGGGGTACGAACTCCATCCTGACAAATGGACAGTNNNNNNNNNNCTAGCAGGATGACTTCGATACCCATGGC
+```
+
+## Output
+
+- DRM.xlsx - 1st sheet - DRM stats, then one sheet per sample
+- freq.xlsx - individual and top allele frequencies