Pinned Repositories
Comparative_Genomics
Micro 612 genomics workshop
Comparative_Genomics-V.2.2017
This is an archived repository of 2017 Micro 612 genomics workshop.
find_hgt_pipeline
compare multiple fasta files using nucmer and extract aligned fragments
Growth-rate-estimate
Calculate Peak to Trough ratio (PTR) from sequencing data.
Growth-rate-estimate_SMAKE
Growth-rate-analysis is a Snakemake workflow to calculate peak to through ratio (PTR - ratio of copy numbers at origin of replication to terminus) from mapped reads coverage.
Nanosake
A Snakemake workflow to basecall, quality control and assemble Nanopore data.
QC-d
Generate Coverage, Quality and Contamination metrics for Sequence data.
QCD_SMAKE
Runs Quality Control workflow on Illumina WGS data
samosa
(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.
snpkit
Modular workflow for Microbial Variant Calling and SNP diagnostics.
alipirani88's Repositories
alipirani88/Comparative_Genomics
Micro 612 genomics workshop
alipirani88/snpkit
Modular workflow for Microbial Variant Calling and SNP diagnostics.
alipirani88/samosa
(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.
alipirani88/Growth-rate-estimate
Calculate Peak to Trough ratio (PTR) from sequencing data.
alipirani88/QC-d
Generate Coverage, Quality and Contamination metrics for Sequence data.
alipirani88/Comparative_Genomics-V.2.2017
This is an archived repository of 2017 Micro 612 genomics workshop.
alipirani88/find_hgt_pipeline
compare multiple fasta files using nucmer and extract aligned fragments
alipirani88/academic-website
alipirani88/Growth-rate-estimate_SMAKE
Growth-rate-analysis is a Snakemake workflow to calculate peak to through ratio (PTR - ratio of copy numbers at origin of replication to terminus) from mapped reads coverage.
alipirani88/Nanosake
A Snakemake workflow to basecall, quality control and assemble Nanopore data.
alipirani88/QCD_SMAKE
Runs Quality Control workflow on Illumina WGS data
alipirani88/alimohammedpirani
alipirani88/bioconda-recipes
Conda recipes for the bioconda channel.
alipirani88/bioinformatics-coffee-hour
Short lessons from FAS Informatics coffee hour
alipirani88/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
alipirani88/gatk
Official code repository for GATK versions 4 and up
alipirani88/Perfect-bacterial-genome-tutorial
alipirani88/Plasmid_Detection_in_MRSA_dataset
alipirani88/prewas
R package to perform data pre-processing for more informative bacterial GWAS
alipirani88/snakemake_teaser
Getting started with Snakemake workflows for automated bioinformatics analysis.
alipirani88/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
alipirani88/starter-hugo-academic
🎓 Hugo Academic Theme 创建一个学术网站. Easily create a beautiful academic résumé or educational website using Hugo, GitHub, and Netlify.
alipirani88/StrainEst
Scripts to generate Strainest Database.
alipirani88/varcall_umich
Variant Calling Pipeline
alipirani88/variant_diagnostics
The scripts in this directory analyses various results generated during variant calling analysis and creates diagnostic plots for exploring variants that were filtered out during the variant filteration step. Generates core SNP vcf and consensus file.