brwnj/umitools

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30
Rank 822,475 (Top 17 %)
Language
Python
License
MIT License
Created over 11 years ago
Updated about 7 years ago

brwnj/umitools

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

bcl2fastq

NextSeq specific bcl2fastq2 wrapper.

covviz

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

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

fastq-join

Squared distance for anchored alignment joiner of ea-utils.

freebayes-nf

a better freebayes-parallel

fqc

Extensible quality control dashboard built around FASTQ assessment.

covdist

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

hundo

Amplicon processing protocols

seqanno

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

polya

scripts associated with identifying polya cleavage preference

blastdbget

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

repertoire

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

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