sajjadasaf's repositories
SYNY
The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
AnnoSINE
SINE annotation tool for plant genomes
assembly-annotation-pipeline
Plant genome assembly and annotation pipeline using snakemake
EasyMicrobiomeR
Using R language in microbiome analysis
Plant_Annotation_TEs
Methods and recipes for Plant Genome Annotation - Transposable Elements
GenoVi
GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
HGTector
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
pyCircos
python Circos
clinker
Gene cluster comparison figure generator
RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
plotsr
Tool to plot synteny and structural rearrangements between genomes
pyGenomeViz
A genome visualization python package for comparative genomics
kalign
A fast multiple sequence alignment program.
sra-tools
SRA Tools
plot_genome_align_fig
Plot genome alignment figure using progressiveMauve & genoPlotR
IRplus
Intelligent Inverted Repeat scoping tool
GBKviz
Easy-to-use web application for visualization and comparison of genomes in Genbank file
WGAVarHunter
Fast and accurate genetic variation identification through whole genome alignment
awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
NOVOPlasty
NOVOPlasty - The organelle assembler and heteroplasmy caller
Nanopore-Workflow
Working pipeline for nanopore + illumina data
MitoFinder
MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
novowrap
Assembly chloroplast genome and validate conformation
ggpubr
'ggplot2' Based Publication Ready Plots
MitoZ
MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
jasp-desktop
JASP aims to be a complete statistical package for both Bayesian and Frequentist statistical methods, that is easy to use and familiar to users of SPSS