Pinned Repositories
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
maliampi
Maximum Likelihood Amplicon Pipeline
phylotypes
Group jplace features into phylogroups
sciluigi
A light-weight wrapper library around Spotify's Luigi workflow system to make writing scientific workflows more fluent, flexible and modular
jgolob's Repositories
jgolob/maliampi
Maximum Likelihood Amplicon Pipeline
jgolob/awsbw
A small CLI utility to view jobs in an AWS batch queue
jgolob/arf
ARF: Algorithmic rRNA Filtering. A hands-off means of obtaining 16s rRNA alleles with valid taxonomic identification
jgolob/phylotypes
Group jplace features into phylogroups
jgolob/academic-kickstart
📝 Easily create a beautiful website using Academic, Hugo, and Netlify
jgolob/d3-scatterplot
A brief demo of D3
jgolob/dada2-combineseqtab
An alternative means of combining many dada2 seqtabs
jgolob/dada2-pplacer
A few utilities to convert dada2 output to be compatible with pplacer and others
jgolob/decard
jgolob/EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
jgolob/FAMLI3
jgolob/goodsfilter
Filter DADA2-style sequence tables using Good's coverage to remove likely contaminant and PCR error sequence variants
jgolob/HmmUFOtu
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
jgolob/humann_nf
Nextflow workflow to run Humann3 on microbiome shotgun metagenomic data
jgolob/immuno-850-scrna
jgolob/lotsoquestions
jgolob/mame
Minimal ASV Making Engine (for 16s rRNA amplicons)
jgolob/medirect
multiprocessed ncbi edirect
jgolob/mothur-nf
MOTHUR 16S analysis software containerized and run via nextflow
jgolob/octapus
Operon ConTextulization Across Prokaryotes to Uncover Synteny
jgolob/PEAR
Pair-End AssembeR
jgolob/ptb_microbiome_samples
jgolob/pycorncob
beta-binomial based testing of count data
jgolob/rome4
Repository of Microbiome Experiments 4: Static-hosted interactive display of microbiome data
jgolob/sepp
Ensemble of HMM methods (SEPP, TIPP, UPP)
jgolob/seqinfo_taxonomy_sync
Oh NCBI taxonomy.
jgolob/singlecellar
jgolob/taxtastic
Create and maintain phylogenetic "reference packages" of biological sequences.
jgolob/transcriptshot
Microbial RNA Seq Pipeline
jgolob/zeroish
Provide a probability of false negatives for compositional count-based data