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3d-dna

3D de novo assembly (3D DNA) pipeline

a-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

alfatclust

Biological sequence clustering tool with dynamic threshold

assembly-stats

Assembly statistic visualisation

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

chorus2

A pipeline to select oligonucleotides for fluorescence in situ hybridization (Oligo-FISH).

clustering-tool-for-nucleotide-sequences-using-laplacian-eigenmaps-and-gaussian-mixture-models

Clustering tool for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Models

dot

Dot: An interactive dot plot viewer for comparative genomics

dot-1

Dot: An interactive dot plot viewer for comparative genomics

eccsplorer

The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read data of amplified circular DNA.

fasta

Perl scripts dealing with fasta files

getorganelle

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

ksrates

ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.

lastz

Program for aligning DNA sequences, a pairwise aligner.

macse_v2_pipelines

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

mcscanx

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

my-first-blog

nextdenovo

Fast and accurate de novo assembler for long reads

nextpolish

Fast and accurately polish the genome generated by long reads.

oligo-melting

Software to estimate oligonucleotide duplexes melting temperature. Includes state-of-the-art monovalent (e.g., Na+) and bivalent (Mg2+) ion correction, formamide (or general denaturant) correction, and melting curve estimation.

ood-fish

Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)

primeval

rasusa

Randomly subsample sequencing reads to a specified coverage

re2_workshops

split-fasta

A Command Line tool for splitting Fasta file with multiple sequences into individual Fasta files.

split_multi_fasta

Split multi fasta file into single fasta files

swap

For website creation practice

tbtools

GUI/CommandLine Tool Box for biologistists to utilize NGS data.