johnurban Goto Github PK

ampure

Script for figuring out AMPure ratios needed for size selection, etc.

autopilot

AutoPiloT : Automated Pilon Tool. Index, map, filter, polish. Repeat.

barseqtools

Code I used/created to analyze bar-seq data.

battery

An automated pipeline for genome assembly evaluations using SLURM.

calcmaxduptags

Toying around with MACS2 calcMaxDupTags model.

clampmassspec2016

Scripts and data needed to reproduce Mass Spec results in CLAMP paper

dbg2olc

deepseep

Various utilities while working with Hi-C data, bedpe, and bed files.

fast5tools

Tools for working with fast5 files (nanopore data).

fftdnamods

A simple python script to work with 2-column tables and do some FFT stuff.

figurelayouts

An R-script with attempts to provide some common layouts for figure making.

gala

Long-reads Gap-free Chromosome-scale Assembler

geckocorrection

geckos need to be shut down

humdrummer

Convert minimap2 transcript alignments to GFF gene models for pleasant viewing in genome browsers like IGV.

interpro-json-extractor

Takes JSON output from InterProScan computed on large proteome file, and outputs all or targeted proteins as individual JSON files for viewing with EBIs JSON viewer.

interpro-what-do-ya-know

One or more scripts for working with the outputs of interproscan.

iwilldeletethis

Here is code from that pper.

lave

Genomics tinkering and plotting functions in R.

lexonsseq2015

Contains notes and custom scripts used to analyze Illumina reads for our NS-seq paper.

macs

MACS -- Model-based Analysis of ChIP-Seq

maligner

A restriction map aligner

mapqcalculators

miniqv

Assembly QV metrics based on fast alignments of a representative sample of reads.

orthochainlinker

poreminion

Additional tools for analyzing Oxford Nanopore minION data

poretools

a toolkit for working with Oxford nanopore data

pufferfish

HMM approaches to genomic and other data. Originally designed to identify DNA "puffs for FISH" in the fungus fly genome.

racoonflyfish

racoonFlyFish: Automated multi-round genome assembly polishing with long reads using combinations of RaCon, Flye, and Medaka.

saltamosca

Tool for querying Fly Atlas 2.

sciara-project-tools

Sciara (pronunciation: Sci as in "Science", "ara" as in Sahara, i.e. Sigh-ara)