ShannonDaddy

multiPrime

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)

swarm

A robust and fast clustering method for amplicon-based studies

GMrepoProgrammableAccess

programmable access to GM repo

umap

Uniform Manifold Approximation and Projection

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads

NanoBLASTer

Basic Local Alignment and Search Tool for Oxford Nanopore Long Sequences

fur

Find Unique genomic Regions

longread_umi

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

pTrimmer

Used to trim off the primer sequence from mutiplex amplicon sequencing

NGTAS_pipeline

Computational pipeline to analyse Next Generation Targeted Amplicon Sequence data

InterVar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline

CellTics

Center for Integrated Diagnostics at Mass General Hospital NGS tools

MrBam

Query Mutated Reads from a Bam

IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

sequana

Sequana: a set of Snakemake NGS pipelines

dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

single-cell-rna-seq

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.

bpipe

Bpipe - a tool for running and managing bioinformatics pipelines