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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.

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

cruzdb

python access to UCSC genomes database

datasets-sars-cov-2

declarative_authorization

An authorization Rails plugin using a declarative DSL for specifying authorization rules in one place

domainator

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

domainator_examples

Advanced examples of how to use the Domainator bioinformatics software suite

duplicates-by-insert-size

Calculates the optical and pcr duplicate rates per insert size bins

em-seq

Tools and Data related to Enzymatic Methylation Sequencing

equalize_bam_reads

Script to equalize the number of reads in a set of bam files

fatools

A Python library for performing DNA fragment-analysis

flexbar

flexible barcode and adapter removal

formtastic

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

galaxy

This branch is the construction zone for building nested workflows

galaxytools

:microscope::books: Galaxy Tool wrappers

hisat2

Graph-based alignment (Hierarchical Graph FM index)

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

igv-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

iims_influenzaa

NEBNext iiMS Influenza A Library Prep for ONT

ionia-corporation.github.io

Error page for NEB freezers that get bounced away from Heroku

iwc

Intergalactic Workflow Commission

large_file_uploader

A simple sinatra tool to accept large uploads in an amazon S3 bucket

lava-dna

Fork from code.google.com/p/lava-dna

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

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.

methylation_tools

A few tools for manipulating methylation call files