Bioinformatics Workbook repository

De-Novo Repeat Discovery Tool

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads

RNA-seq data analysis course on Artemis HPC

Diploid genome assembly analysis tools

An integrated high performance bioinformatics toolkit

Dotplot large Genomes in an Interactive, Efficient and Simple way

Fast alignment and preprocessing of chromatin profiles

k-mer based assembly evaluation

Generate an interactive dot plot from mummer or minimap alignments

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Yet another Hi-C scaffolding tool

Yet another Hi-C scaffolding tool

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

This is a method to find telomeres and centromeres in plants.

Centromics: visualing centromeres with multiple omics data

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

A python script for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files

3D de novo assembly (3D DNA) pipeline

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

work note

TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to major clades/families of transposon Open Reading Frames.

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust

Mapping pipeline for data generated using Arima-HiC