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
Pinned Repositories
bedtk
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
bioawk
BWK awk modified for biological data
bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics-workbook
Bioinformatics Workbook repository
canu
A single molecule sequence assembler for genomes large and small.
chat-gpt-games
Prompts for playable games in ChatGPT
ComputationalTools_Lessons
DiscoverY
K-mer based classifier for Y-contig identification from Whole Genome Assemblies
dN-dS_using_PAML
How to calculate dN/dS using PAML software
tcas_india_genome_assembly
shivanshss's Repositories
shivanshss/tcas_india_genome_assembly
shivanshss/bedtk
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
shivanshss/bioawk
BWK awk modified for biological data
shivanshss/bioconda-recipes
Conda recipes for the bioconda channel.
shivanshss/bioinformatics-workbook
Bioinformatics Workbook repository
shivanshss/canu
A single molecule sequence assembler for genomes large and small.
shivanshss/chat-gpt-games
Prompts for playable games in ChatGPT
shivanshss/DiscoverY
K-mer based classifier for Y-contig identification from Whole Genome Assemblies
shivanshss/dN-dS_using_PAML
How to calculate dN/dS using PAML software
shivanshss/extra_NGS_related
This repository contains simple codes and functions often used in NGS (next Gen seq) and TGS (Third gen seq) analyses
shivanshss/fasta_summary
Summarize the contents of FASTA files.
shivanshss/fasta_validator
C code to validate a fasta file
shivanshss/fastq2highQualVCF
Scripts to process reads from FASTQ to VCF including filters
shivanshss/fun_projects
This repository contains some random fun projects
shivanshss/GAAS
Genome Assembly and Annotation Service code
shivanshss/Genome_Assembly_Assessment
shivanshss/GenomeAssemblyTools
Genome Assembly Tools
shivanshss/MAKER-genome-annotations-tutorial
Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support
shivanshss/mauve
A genome alignment and visualization system
shivanshss/mummer4
Mummer alignment tool
shivanshss/PhylOligo
Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.
shivanshss/seqtk
Toolkit for processing sequences in FASTA/Q formats
shivanshss/Simple_Script
pipeline and tools for personal use
shivanshss/Statistical_tests
This is a repository containing different statistical tests written in simple R scripts that I often use when processing data obtained in the lab.
shivanshss/summarize-snps-with-gff
shivanshss/syntenyPlotByR
plot genome alignment synteny
shivanshss/tcas_india_divergence_selection
This repository contains scripts, test data and sample output files for analysis done for chapter 2 of my PhD thesis
shivanshss/timeline-biology
This is a code to make a timeline in biology.
shivanshss/TRF-mod
Tandem Repeats Finder: a program to analyze DNA sequences
shivanshss/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings