New England Biolabs Inc.

plate-map

A flexible tool for defining the contents of 96 well plates.

EM-seq

Tools and Data related to Enzymatic Methylation Sequencing

ampseer

Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.

domainator

A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.

VarSkip

VarSkip multiplex PCR designs for SARS-CoV-2 sequencing

mark-nonconverted-reads

This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.

primer_monitor

a service to allow people to register primers to be monitored for intersecting variants and be notified if new variants arise

iiMS_InfluenzaA

NEBNext iiMS Influenza A Library Prep for ONT

picard_bcl_to_fastq

Demultiplexes a MiSeq, NextSeq or HiSeq run using Picard's IlluminaBasecallsToFastq

seq-results-deprecated

Deprecated: Web interface to manage a database of sequence results (merged into ngs-aggregate-results)

tasmanian-mismatch

Analysis of artifacts in high throughput sequencing data from genomic DNA.

wps-ss-generator

This is an attempt to streamline 96 well assembly / combination of ONT WPS submissions to the Sequencing Core

FFPE_nextflow_workflow

Workflow to analyze FFPE ngs data

opentrons

Collection of scripts which can be used in relation to Opentrons OT-2 Liquid Handling Robot

uncleShiny

A dashboard for Unchained Labs Uncle data visualization written in R using Shiny.

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

Cas-PAM-cleavage-analysis

datasets-sars-cov-2

domainator_examples

Advanced examples of how to use the Domainator bioinformatics software suite

fatools

A Python library for performing DNA fragment-analysis

formtastic

A Rails form builder plugin with semantically rich and accessible markup.

iwc

Intergalactic Workflow Commission

low_bismap_methyl_calls

Tools to assess called methylation in low mappability regions (as defined by bismap). Aligner MapQ does not always align with low mappability

neb-galaxy-workflows

Galaxy Workflows

ngslite

Light-weight functions for next-generation sequencing (NGS) data analysis

poreCov

SARS-CoV-2 workflow for nanopore sequence data

primer-schemes

Primer schemes for real-time genome epidemiology

rsvAB-sequencing

NEBNext RSV A/B Multiplex PCR sequencing primers

unclePy

A parser for Unchained Labs Uncle HDF5 binary files written in Python.

usegalaxy-tools

usegalaxy.* common tools