answer_looker's repositories
notepad-plus-plus
Notepad++ official repository
MARVEL
The MARVEL assembler
gatk
Official code repository for GATK versions 4 and up
ssr_finder
Find simple repeat sequences in the assembly genome and design proper primers for simple repeat sequences in 10 steps ssr_finder
PopLDdecay
PopLDdecay: A new simple and efficient software for Linkage Disequilibrium Decay analysis based Variant Call Format
canu
A single molecule sequence assembler for genomes large and small.
arcs
Scaffold genome sequence assemblies using 10x Genomics data
pilon
Pilon is an automated genome assembly improvement and variant detection tool
maize_v4_TE_annotation
scripts and intermediate files used to annotate TEs in Jiao et al.
phenolyzer
phenotype-based prioritization of candidate genes for human diseases
MECAT
MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
genome-scripts
Genome Scripts used in fungal comparative genomics
cDNA_primer
Scripts for processing PacBio transcriptome (Iso-Seq) data
PhylOligo
Bioinformatics / Explore oligonucleotide composition similarity between assembly contigs or scaffolds to detect contaminant DNA.
diamond
Accelerated BLAST compatible local sequence aligner.
flo
Same species annotation lift over pipeline.
Orthograph
Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models
CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
HomBlocks
HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching
proovread
PacBio hybrid error correction through iterative short read consensus
HpcGridRunner.github.io
web documentation for HpcGridRunner
gatk-protected
GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only
galaxytools
Galaxy Tool wrappers
TARGeT
Tree Analysis of Related Genes and Transposons
paraat
paraat2.0 code and files for creation of dockerfile
kaks-calculator
Automatically exported from code.google.com/p/kaks-calculator
ltr-finder
Automatically exported from code.google.com/p/ltr-finder
Irys-scaffolding
scripts to parse IrysView output