Pinned Repositories
seqcover
seqcover allows users to view coverage for hundreds of genes and dozens of samples
bcl2fastq
NextSeq specific bcl2fastq2 wrapper.
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
fastq-join
Squared distance for anchored alignment joiner of ea-utils.
fastq-multx
Demultiplexes a fastq.
idplot
compare sequences to a shared root reference sequence.
smoove-nf
Nextflow implementation of the smoove workflow and other tools for SV calling and QC
umitools
Tools to handle reads sequenced with unique molecular identifiers (UMIs).
bedqc
BED QC tool (in the making)
brwnj's Repositories
brwnj/umitools
Tools to handle reads sequenced with unique molecular identifiers (UMIs).
brwnj/fastq-join
Squared distance for anchored alignment joiner of ea-utils.
brwnj/fqc
Extensible quality control dashboard built around FASTQ assessment.
brwnj/blastdbget
Download Blast databases from ftp.ncbi.nlm.nih.gov/blast/db, validate, and extract.
brwnj/hundo
Amplicon processing protocols
brwnj/polya
scripts associated with identifying polya cleavage preference
brwnj/repertoire
Pipelines for assembling and assessing T and B cell receptor repertoires.
brwnj/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.
brwnj/gdemux
demultiplex into groups (subsets) rather than individual sample files, by barcode
brwnj/amazon-glacier-cmd-interface
Command line interface for Amazon Glacier
brwnj/asthma
RNA-seq quantifications: gene expression responses to human rhinovirus infection for 6 asthmatic and 6 non-asthmatic donors (SRP046226)
brwnj/biom-format
The Biological Observation Matrix (BIOM) Format Project
brwnj/boto
Python interface to Amazon Web Services
brwnj/cmaputil
brwnj/ConfigArgParse
A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
brwnj/cookiecutter-snakemake-workflow
A cookiecutter template for Snakemake workflows
brwnj/cu_projects
brwnj/DETECT-v2
Version 2 of the Density Estimation Tool for Enzyme ClassificaTion: scripts for enzyme annotation and pipeline for making the DETECT database
brwnj/fastedit
Quickly alter the headers of a manageable number of fasta entries using a CSV.
brwnj/fastqp
Simple FASTQ quality assessment using Python
brwnj/gpd
JGI Genome Portal Downloader: facilitating downloads via XML
brwnj/interaction_network
brwnj/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
brwnj/notebooks
brwnj/peaktools
brwnj/pyani
Python module for average nucleotide identity analyses
brwnj/pyflow-epilogos
snakemake workflow for epilogos on chromHMM data
brwnj/sequana
Sequana: a set of Snakemake NGS pipelines
brwnj/sequence_clustering
De novo identification and quantification of sequence data.
brwnj/slurm
Cookiecutter for snakemake slurm profile