alipirani88/Nanosake

A Snakemake workflow to basecall, quality control and assemble Nanopore data.

Language: Python - Size: 65.2 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 2

alipirani88/snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

Language: Python - Size: 60.9 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 4 - Forks: 4

alipirani88/assemblage

Workflow to assemble and annotate bacterial genomes.

Language: Python - Size: 469 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 2

alipirani88/Comparative_Genomics

Micro 612 genomics workshop

Language: Shell - Size: 42 MB - Last synced: 3 months ago - Pushed: about 3 years ago - Stars: 35 - Forks: 32

alipirani88/QCD_SMAKE

Runs Quality Control workflow on Illumina WGS data

Language: Python - Size: 2.74 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

alipirani88/Growth-rate-estimate 📦

Calculate Peak to Trough ratio (PTR) from sequencing data.

Language: Python - Size: 486 KB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 2 - Forks: 1

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.

Language: Jupyter Notebook - Size: 4.14 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

alipirani88/alimohammedpirani

Language: HTML - Size: 10.9 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

alipirani88/Plasmid_Detection_in_MRSA_dataset

Language: Jupyter Notebook - Size: 1.26 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

alipirani88/prewas Fork of Snitkin-Lab-Umich/prewas

R package to perform data pre-processing for more informative bacterial GWAS

Language: R - Size: 924 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

alipirani88/QC-d

Generate Coverage, Quality and Contamination metrics for Sequence data.

Language: Jupyter Notebook - Size: 16.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 2 - Forks: 2

alipirani88/gatk Fork of broadinstitute/gatk

Official code repository for GATK versions 4 and up

Size: 429 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

alipirani88/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 368 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

alipirani88/varcall_umich 📦

Variant Calling Pipeline

Language: Python - Size: 142 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 2

alipirani88/Comparative_Genomics-V.2.2017 📦

This is an archived repository of 2017 Micro 612 genomics workshop.

Size: 20.9 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

alipirani88/Perfect-bacterial-genome-tutorial Fork of rrwick/Perfect-bacterial-genome-tutorial

Size: 540 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

alipirani88/find_hgt_pipeline

compare multiple fasta files using nucmer and extract aligned fragments

Language: Python - Size: 59.6 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

alipirani88/samosa

(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.

Language: Jupyter Notebook - Size: 20.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

alipirani88/snippy Fork of tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Size: 125 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

alipirani88/starter-hugo-academic Fork of wowchemy/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.

Size: 10.8 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

alipirani88/snakemake_teaser

Getting started with Snakemake workflows for automated bioinformatics analysis.

Language: Jupyter Notebook - Size: 52.1 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

alipirani88/bioinformatics-coffee-hour Fork of harvardinformatics/bioinformatics-coffee-hour

Short lessons from FAS Informatics coffee hour

Size: 2.31 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

alipirani88/StrainEst

Scripts to generate Strainest Database.

Language: Python - Size: 7.81 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

alipirani88/academic-website Fork of eteitelbaum/academic-website

Size: 78.1 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

alipirani88/dna-seq-gatk-variant-calling Fork of snakemake-workflows/dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

Size: 9.18 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0