Discover brwnj/covdist Open Source project by Joe Brown (@brwnj)

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HTML
License
MIT License
Created about 3 years ago
Updated over 1 year ago

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

bcl2fastq

NextSeq specific bcl2fastq2 wrapper.

Python

covviz

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

HTML

fastq-multx

Demultiplexes a fastq.

C++

umitools

Tools to handle reads sequenced with unique molecular identifiers (UMIs).

Python

idplot

compare sequences to a shared root reference sequence.

HTML

smoove-nf

Nextflow implementation of the smoove workflow and other tools for SV calling and QC

Python

fastq-join

Squared distance for anchored alignment joiner of ea-utils.

C++

freebayes-nf

a better freebayes-parallel

Nextflow

fqc

Extensible quality control dashboard built around FASTQ assessment.

JavaScript

hundo

Amplicon processing protocols

Python

seqanno

Retrieves read counts originating at a given genomic sequence and allows further characterization.

Python

polya

scripts associated with identifying polya cleavage preference

Python

blastdbget

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

Python

repertoire

Pipelines for assembling and assessing T and B cell receptor repertoires.

Perl

relatively

📊 Plotly abundance figure with absolute and relative abundances across a hierarchy

Jupyter Notebook

binder

mybinder.org - open testing.

Jupyter Notebook

gdemux

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

Python

brwnj/covdist

brwnj

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