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amazon-glacier-cmd-interface

Command line interface for Amazon Glacier

arq5x.github.io

asthma

RNA-seq quantifications: gene expression responses to human rhinovirus infection for 6 asthmatic and 6 non-asthmatic donors (SRP046226)

bcl2fastq

NextSeq specific bcl2fastq2 wrapper.

binder

mybinder.org - open testing.

biom-format

The Biological Observation Matrix (BIOM) Format Project

blastdbget

Download Blast databases from ftp.ncbi.nlm.nih.gov/blast/db, validate, and extract.

boto

Python interface to Amazon Web Services

bpbio

a single binary with many useful genomics subtools.

brwnj

cmaputil

configargparse

A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

covdist

simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

crest

CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification of environmental marker genes from sequencing-based community profiling studies.

cu_projects

detect-v2

Version 2 of the Density Estimation Tool for Enzyme ClassificaTion: scripts for enzyme annotation and pipeline for making the DETECT database

dotfiles

.files, including ~/.osx — sensible hacker defaults for OS X

facets-nf

nextflow implementation of the facets data flow.

fastedit

Quickly alter the headers of a manageable number of fasta entries using a CSV.

fastq-join

Squared distance for anchored alignment joiner of ea-utils.

fastq-multx

Demultiplexes a fastq.

fastqp

Simple FASTQ quality assessment using Python

fqc

Extensible quality control dashboard built around FASTQ assessment.

freebayes-nf

a better freebayes-parallel

gdemux

demultiplex into groups (subsets) rather than individual sample files, by barcode

ggd-recipes

conda recipes for genomic data

github-vscode-theme-iterm

:octocat: GitHub VS Code Theme for iTerm

gpd

JGI Genome Portal Downloader: facilitating downloads via XML