atotickov

umis

Tools for processing UMI RNA-tag data

zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

masurca

BuscoClade

Snakemake pipeline to construct species phylogenies using BUSCOs

ITSpipe

ITS mapping and variant call

Biocrutch

Various bioinformatics scripts

gatk

Official code repository for GATK versions 4 and up

make_lastz_chains

Portable solution to generate genome alignment chains using lastz

transcriptomics.msu

Materials for Transcripromics Data Analysis course at Moscow State University

ms-PSMC

Useful scripts when applying the psmc to simulated data with ms

vertebrate_rate

Method used in the study on germline mutation rate estimation in 68 species of vertebrates.

psmc-python

A reimplementation of a classical PSMC method in python for educational purposes

pante

A pipeline for predicting and masking transposable elements in multiple genomes.

telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

EDTA

Extensive de-novo TE Annotator

krait

An ultrafast tool for genome-wide survey of microsatellites and primer design

TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.

EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline

trails

Tree reconstruction of ancestry using incomplete lineage sorting

full_spectrum_bioinformatics

An open-access bioinformatics text

srf

SRF: Satellite Repeat Finder

repex_tarean

RepeatExplorer2 singularity definition

Worm-nomics

Workflow, scripts and analyses described in Adams et al 2023

gamma_smc

2vcf

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

DTC_Scripts

Scripts to Analyze DTC Sequencing and Genotyping Data (and some comparisons to Veritas WGS data)

ung

Экспорт сведений о родственниках из личного кабинета Генотек

Scripts-for-RepeatExplorer2-parsing