linxingchen

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

CRISPR

crispr analyses

FASTA

basic scripts for fasta file

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

General

any general scripts

noveltree

NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

PlasmidHunter

This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.

pullseq

Utility program for extracting sequences from a fasta/fastq file

shrinksam

C++ program to shrink the SAM file after a read-mapping

sickle

Windowed Adaptive Trimming for fastq files using quality

linxingchen/cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

linxingchen/FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

linxingchen/noveltree

NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

linxingchen/PlasmidHunter

This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.

linxingchen/pprodigal

Python3 wrapper for parallelized gene prediction using Prodigal

linxingchen/prodigal-gv

A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

linxingchen/astra

pyHMMer-based sequence search and retrieval tool.

linxingchen/bioconda-recipes

Conda recipes for the bioconda channel.

linxingchen/Carter-and-Olm-Cell-2023---db-info

README for Zenodo archive associated with publication Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

linxingchen/chainsaw

Rapidly Search and Hunt through Windows Forensic Artefacts

linxingchen/Complete-Python-3-Bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

linxingchen/contig-extender

linxingchen/defense-finder

Systematic search of all known anti-phage systems.

linxingchen/DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

linxingchen/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

linxingchen/foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

linxingchen/genomad

geNomad: Identification of mobile genetic elements

linxingchen/Jorg

MAG Circularization Method

linxingchen/MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data

linxingchen/MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

linxingchen/nanopore_script

A snakemake assembly pipeline for hybrid metagenome sequencing

linxingchen/PhaGCN2.0

linxingchen/PhaGCN_newICTV

Update model for ICTV2022

linxingchen/phamb

Downstream processing of VAMB binning for Viral Elucidation

linxingchen/PlasX

PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

linxingchen/RoseTTAFold-All-Atom

linxingchen/sphae

NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!

linxingchen/umap

Uniform Manifold Approximation and Projection

linxingchen/ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

linxingchen/vsearch

Versatile open-source tool for microbiome analysis