52teth's repositories
oh-my-zsh
A delightful community-driven (with 1,200+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
bamdst
a lightweight bam file depth statistical tool
cheatsheets
RStudio Cheat Sheets
MONOD2
MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
Jellyfish
A fast multi-threaded k-mer counter
FALCON
FALCON: experimental PacBio diploid assembler
GenomicConsensus
PacBio® variant and consensus caller
miniasm
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
TransDecoder
TransDecoder source
IsoSeq_SA3nUP
Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond
Cogent
Coding Genome Reconstruction using Iso-Seq data
BFAST
BFAST: the Blat-like Fast Accurate Search Tool
pacbio_variant_caller
SMRT-SV: Structural variant and indel caller for PacBio reads
rCharts
Interactive JS Charts from R
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing sequencing data
khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
PacBio-generic
General (non-project specific) collection of scripts
proovread
PacBio hybrid error correction through iterative short read consensus
gffcompare
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
cDNA_primer
Scripts for processing PacBio transcriptome (Iso-Seq) data
IsoView
Visualization and clustering of DNA transcript data
Irys-scaffolding
scripts to parse IrysView output