shivanshss
I am a research scholar. I am interested in high-throughput genomics. Here is a collection of scripts and tools I have used/made
Bangalore, India
shivanshss's Stars
Illumina/manta
Structural variant and indel caller for mapped sequencing data
gpertea/gffcompare
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
TobyBaril/EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
genome/breakdancer
SV detection from paired end reads mapping
shingocat/lrscaf
TGS scaffolding
koadman/mauve
A genome alignment and visualization system
BGI-Qingdao/ProcessGroupMonitor
A simple tool to monitor a process group and record its CPU, MEM and time cost.
mkirsche/Grafter
Scaffolding with Ultralong Reads
makovalab-psu/DiscoverY
K-mer based classifier for Y-contig identification from Whole Genome Assemblies
beausoleilmo/Rsimulation
A lesson on how to use simulations in R
chienchi/MUMmer
version 3.23
NCBS-students/Sympotein
Sympotein event at NCBS
abhishekkmukherjee/Philosophy
:octocat: A list of philosophy books and resources.
beausoleilmo/Genomic_island
This repository contains scripts related to the analysis of genomic islands of divergence in Darwin's finches
beausoleilmo/ggcoverage
Visualize and annotate genomic coverage with ggplot2
beausoleilmo/timeline-biology
This is a code to make a timeline in biology.
botond-sipos/csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
gacrestani/pdf2xlsx_rema
Takes a PDF and gives .xlsx tables from each one of the PDF tables.
GiannosLouloudis/N-island_Discovery
Parse through assembled chromosomes and identify the coordinates of N-islands greater than 100-N long.
jebrosen/wiki
Wiki.js | A modern and powerful wiki app built on Node.js
lillux/stanford-tensorflow-tutorials
This repository contains code examples for the Stanford's course: TensorFlow for Deep Learning Research.
mkirsche/VariantValidator
rmhubley/neutral-model-estimator
Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
TobyBaril/hoverflyAnnotation2023
Workflow for annotation of Hoverfly genome (GCA_945859705.1) with D. melanogaster homologs
zhangwenda0518/dotPlotly
Generate an interactive dot plot from mummer or minimap alignments
zhangwenda0518/EasySpeciesTree
Easily construct the ML species tree with single-copy gene shared by different species.
zhangwenda0518/GCE
GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.
zhangwenda0518/Genome_Assembly_Assessment
zhangwenda0518/JaltGenome
Raw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.
zhangwenda0518/TrimmingPipeline
Python pipeline for PBS script creation for trimming RNA-Seq data with rCorrector, BBDuk, and generating FastQC reports