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Tauqeer Alam's Projects

abricate icon abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

abritamr icon abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

afa-core icon afa-core

Generates lists of core/non-core sites from a multi-FASTA alignment for ClonalFrameML

agrvate icon agrvate

Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.

amplikate icon amplikate

📢🎯 Generic typing tool from amplicons and/or in silico PCR

andi icon andi

♥ Efficient Estimation of Evolutionary Distances

ani_calculator icon ani_calculator

This program performs a given ANI method (ANIb or ANIm) on a set of input files or downloads a group of files by syncronizing to ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ and by searching for the DOWNLOADTOKEN

asap icon asap

A scalable bacterial genome assembly, annotation and analysis pipeline

assembly_stats icon assembly_stats

Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.

bacterialgwas icon bacterialgwas

A pipeline for performing genome-wide association tests for bacterial genomes.

bactofidia icon bactofidia

bacterial assembly and basic analysis using bioconda and Snakemake

bactopia icon bactopia

An extensive workflow to process Illumina sequencing for bacterial genomes.

bactspeciesid icon bactspeciesid

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

bash-oneliner icon bash-oneliner

A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

bioinfo-scripts icon bioinfo-scripts

Collection of bioinformatics utility scripts, mostly written in Bioperl

bioinfokit icon bioinfokit

Bioinformatics data analysis and visualization toolkit

bohra icon bohra

A pipeline for bioinformatics analysis of bacterial genomes

cafe icon cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

clinker icon clinker

Gene cluster comparison figure generator

cogclassifier icon cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

coinfinder icon coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.

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