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100-gcc-tips

A collection of gcc tips. 100 maybe just mean many here.

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

awesome-cheatsheets

超级速查表 - 编程语言、框架和开发工具的速查表，单个文件包含一切你需要知道的东西 :zap:

bacterialgwas

A pipeline for performing genome-wide association tests for bacterial genomes.

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

big-map

bin

scripts

bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

blast-utils

utils to manipulate blast6out files

blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

cactus

Official home of genome aligner based upon notion of Cactus graphs

call_snp_pipeline

Run the freebayes pipeline automatically, include bwa,sam2bam,sort,rmdup,addrg,freebayes...

carveme

CarveMe: genome-scale metabolic model reconstruction

cellphonedb

clinker

Gene cluster comparison figure generator

coverm

Read coverage calculator for metagenomics

crass

The CRISPR assembler

crisprlong

tools for characterizing crispr arrays using long reads

deepmod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

demovir

Taxonomic classification of viruses at Order and Family level

domain_classifier

Classify sequence to a taxonomic domain using PFAM domains

dotplotly

Generate an interactive dot plot from mummer or minimap alignments

dragonstar2019

drep

Rapid comparison and dereplication of genomes

dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

enrichment4gtex_clusterprofiler

reproduce the functional enrichment analysis presented in GTEx paper using clusterProfiler/DOSE

epigene_pipeline