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microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

microbiomeviz

Visualize microbiome data with black magic ggtree

microdecon

An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

miqtl_cookbook

ml_human_gut

motus_v2

motus - a tool for marker gene-based OTU (mOTU) profiling

msisensor2

Microsatellite instability (MSI) detection for tumor only data.

mtd

MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data

mycobiome

Pan-cancer mycobiome atlas

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

picard

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

picrust

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

picrust2

Code, unit tests, and tutorials for running PICRUSt2

pipeline_trans_lcz

The pipeline uncovered the dynamic replication and transcription of Lactobacillus casei Zhang in the human gut

plsdabatch

Development repository for R package 'PLSDAbatch ' hosted on Bioconductor.

probiotics-snv-meta

In this study, we annotated the SNV of the gut microbiota after probiotics treatment.

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

qiime2

Official repository for the QIIME 2 framework.

qiime2chinesemanual

QIIME 2中文文档(QIIME 2 Chinese Manual)

reutils

Talk to the NCBI EUtils

rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

roary

Rapid large-scale prokaryote pan genome analysis

run_dbcan

Run_dbcan V2, using genomes/metagenomes/proteomes of any orgaisms(prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

sahmi

SAHMI

saige

Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

saige-1

Development for SAIGE and SAIGE-GENE(+)

scrub

sgvfinder

sickle

Windowed Adaptive Trimming for fastq files using quality