Pinned Repositories
AcinetobacterPlasmidTyping
AgingClock
BackBLAST_Reciprocal_BLAST
This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.
bacterialGWAS
A pipeline for performing genome-wide association tests for bacterial genomes.
bactopia
A flexible pipeline for complete analysis of bacterial genomes
biocode
Bioinformatics code libraries and scripts
bit
Bioinformatics Tools
cactus
Official home of genome aligner based upon notion of Cactus graphs
CART-python
python implementation of the CART algorithm
circlator
A tool to circularize genome assemblies
germant13's Repositories
germant13/AcinetobacterPlasmidTyping
germant13/BackBLAST_Reciprocal_BLAST
This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.
germant13/biocode
Bioinformatics code libraries and scripts
germant13/cactus
Official home of genome aligner based upon notion of Cactus graphs
germant13/clinker
Gene cluster comparison figure generator
germant13/drep
Rapid comparison and dereplication of genomes
germant13/enveomics
Scripts and reference libraries at Kostas lab.
germant13/EukProt
Helper Perl scripts and tree files associated with the EukProt database of genome-scale eukaryotic protein sequence data sets.
germant13/FastANI
Fast Whole-Genome Similarity (ANI) Estimation
germant13/GeneLab_Data_Processing
germant13/groves
Tools for analyzing trees
germant13/hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
germant13/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
germant13/iFeature
iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates fi
germant13/iFeatureOmega-GUI
iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versio
germant13/mummer2circos
Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
germant13/NGSEPcore
NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).
germant13/Online_R_learning
Online R learning for applied statistics
germant13/OpenVoice
Instant voice cloning by MyShell.
germant13/PanACoTA
PANgenome with Annotations, COre identification, Tree and corresponding Alignments
germant13/panstripe
post processing of bacterial pangenome gene presence/absence matrices
germant13/phast
PHAST
germant13/pocp
Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.
germant13/ProkFunFind
A tool for identifying and analyzing functions in microbial genomes.
germant13/protein_analysis_tools
USAlign, Rosetta, Amber and other apps script analysis
germant13/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
germant13/Shewanella_genomics
germant13/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
germant13/SVbyEye
germant13/Traglia2023_AbST2_SARS
Genomic Comparative analysis of two multi-drug resistance (MDR) Acinetobacter baumannii clinical strains assigned to international clonal lineage II recovered pre- and post-COVID-19 pandemic