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academic-kickstart

📝 Easily create a beautiful website using Academic, Hugo, and Netlify

arf

ARF: Algorithmic rRNA Filtering. A hands-off means of obtaining 16s rRNA alleles with valid taxonomic identification

awsbw

A small CLI utility to view jobs in an AWS batch queue

barcodecop

Enforce barcode match stringency and read quality in demultiplexed MiSeq reads

bioscons

Extends the scons build tool for reproducible workflows in bioinformatics.

bucket_command_wrapper

Wrapper to facilitate downloading / uploading files from buckets (i.e. S3) into containers (i.e. docker) and running an arbitrary command.

consecution

:trolleybus: A pipeline abstraction for Python

d3-scatterplot

A brief demo of D3

dada2-combineseqtab

An alternative means of combining many dada2 seqtabs

dada2-pplacer

A few utilities to convert dada2 output to be compatible with pplacer and others

decard

docker-sra

Get data from SRA

emirge

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

famli3

goodsfilter

Filter DADA2-style sequence tables using Good's coverage to remove likely contaminant and PCR error sequence variants

hmmufotu

An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing

humann_nf

Nextflow workflow to run Humann3 on microbiome shotgun metagenomic data

immuno-850-scrna

jplacestats

Retrieve stats on the placement quality

lotsoquestions

maliampi

Maximum Likelihood Amplicon Pipeline

mame

Minimal ASV Making Engine (for 16s rRNA amplicons)

medirect

multiprocessed ncbi edirect

mothur-nf

MOTHUR 16S analysis software containerized and run via nextflow

octapus

Operon ConTextulization Across Prokaryotes to Uncover Synteny

pear

Pair-End AssembeR

phylotypes

Group jplace features into phylogroups

pplacer

Phylogenetic placement and downstream analysis

ptb_microbiome_samples

pycorncob

beta-binomial based testing of count data