• Stars
    star
    1
  • Language
    Python
  • Created over 4 years ago
  • Updated over 4 years ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Pipleine code for "Sensitive identification of bacterial DNA in clinical specimens by broad range 16S rRNA enrichment"

More Repositories

1

argparse-bash

Use python's argparse module in shell scripts
Shell
167
star
2

org-export

batch export of org-mode files from the command line
Emacs Lisp
64
star
3

bioscons

Extends the scons build tool for reproducible workflows in bioinformatics.
Python
17
star
4

.emacs.d

My emacs configuration
Emacs Lisp
16
star
5

alnvu

Reformat and condense multiple sequence alignments to highlight variability
Python
7
star
6

Seq

(abandoned) python utilities for manipulation of biological sequences
Python
7
star
7

swarmwrapper

Wraps swarm to perform pooled dereplication
Python
3
star
8

mkvenv

A wrapper for virtualenv, pip, and wheel
Python
3
star
9

rvenv

Install and manage R packages in a python virtualenv.
R
2
star
10

emacs-config

My emacs configuration, take 2
Emacs Lisp
2
star
11

barcodecop

Enforce barcode match stringency and read quality in demultiplexed MiSeq reads
Python
2
star
12

fastalite

Simplest possible fasta/fastq parser
Python
2
star
13

opiates

Automated QA for a clinical LC/MS urine opaites assay
Python
2
star
14

borborygmi

A blog built using emacs org-mode and Pelican
HTML
2
star
15

ya16sdb

A curated subset of 16S rRNA sequences from NCBI
Python
2
star
16

pymenu

Provides a simple, interactive text-based user interface
Python
2
star
17

unittools

Lightweight utility for running python unit tests
Python
2
star
18

uwgroups

Python library and CLI for UW Groups API
Python
1
star
19

mypy

Configuration for my python environment
Shell
1
star
20

dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
Python
1
star
21

ungapatchka

A python project template with bells and whistles
Python
1
star
22

deduplicate

Remove duplicates from collections of biological sequences
1
star
23

lab-software-whitepaper

A whitepaper describing software development best practices for the clinical laboratory
TeX
1
star