nebiolabs

plate-map

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

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.

VarSkip

VarSkip multiplex PCR designs for SARS-CoV-2 sequencing

EM-seq

Tools and Data related to Enzymatic Methylation Sequencing

domainator

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

nebnext-single-cell-rna-seq

Adapter trimming directions for NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina

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.

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.

uncleShiny

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

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

Cas-PAM-cleavage-analysis

checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

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.

galaxytools

:microscope::books: Galaxy Tool wrappers

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

opentrons

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

poreCov

SARS-CoV-2 workflow for nanopore sequence data

primer-schemes

Primer schemes for real-time genome epidemiology

unclePy

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

usegalaxy-tools

usegalaxy.* common tools