Pinned Repositories
annie
annie = ANNotation Information Extractor
bioinformatics-tools
Awk, bash, python scripts for processing NGS data
GAG
Generates an NCBI .tbl file of annotations on a genome.
HamstrFiltr
Start with a genome, single copy orthologs and SNPs; end with a list of the SNPpiest single copy ortholog exons in the genome
name_change
Tool to rename a list of names in a file from a provided dictionary file
OrthoMCL-docker
An OrthoMCL setup in a docker image
pileup_analyzer
Python program to do wizardly stuff to samtools mpileup output
PyLep_MAP
Python Bioinformatics pipeline for Lep-MAP, rQTL, Super-scaffold assemblies
snp_explorer
Console-based Python program for filtering vcf files
transvestigator
Validates transcriptome and prepares it for submission to the NCBI
genomeannotation's Repositories
genomeannotation/GAG
Generates an NCBI .tbl file of annotations on a genome.
genomeannotation/bioinformatics-tools
Awk, bash, python scripts for processing NGS data
genomeannotation/annie
annie = ANNotation Information Extractor
genomeannotation/OrthoMCL-docker
An OrthoMCL setup in a docker image
genomeannotation/transvestigator
Validates transcriptome and prepares it for submission to the NCBI
genomeannotation/PyLep_MAP
Python Bioinformatics pipeline for Lep-MAP, rQTL, Super-scaffold assemblies
genomeannotation/HamstrFiltr
Start with a genome, single copy orthologs and SNPs; end with a list of the SNPpiest single copy ortholog exons in the genome
genomeannotation/name_change
Tool to rename a list of names in a file from a provided dictionary file
genomeannotation/454_data_scripts
Useful code for parsing 454 data in FORTRAN
genomeannotation/biosoftnamegen
Generates Amazing Ideas for Bioinformatics Software Projects
genomeannotation/capn_primer
Designs and validates primers, sails the seven seas.
genomeannotation/fasta_length
Generates sequence length histogram from several fastas
genomeannotation/FastaLocTable
Writes a table of fasta sequence bases at locations
genomeannotation/genomeannotation.github.io
genomeannotation/heatmap
Generates a heat map from a matrix of numbers
genomeannotation/loci_translate
Translates loci using an .agp file
genomeannotation/MoanaPipelines
Pipelines to analyze and correct reads, count kmers and assemble genomes -- meant to run on our local cluster
genomeannotation/no_bad_products
Cleans up annotation syntax to conform to NCBI standards
genomeannotation/ped_tools
Tools to tweak and validate and reformat PED files
genomeannotation/PySTACKS
Python STACKS pipeline
genomeannotation/reformat
Tool that outputs structure and pedegree files from .vcf, plink.map, plink.ped, hapmap files
genomeannotation/seq_coverage
Calculates coverage of sequence across fasta files
genomeannotation/taskmaker
Helper program to create SGE job scripts
genomeannotation/unigener
genomeannotation/WhosYourDaddy
A simple tool to find a Father's genome if it has gone missing
genomeannotation/window
Scripts for breaking genomic data into windows
genomeannotation/xxxxxxxxxxgap4t
top secret
genomeannotation/YART
yet another reformatting tool
genomeannotation/yomama
Deprimers your things
genomeannotation/yotools
A bunch of tools for deoligoing stuff