genomeannotation's repositories
bioinformatics-tools
Awk, bash, python scripts for processing NGS data
OrthoMCL-docker
An OrthoMCL setup in a docker image
transvestigator
Validates transcriptome and prepares it for submission to the NCBI
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
454_data_scripts
Useful code for parsing 454 data in FORTRAN
biosoftnamegen
Generates Amazing Ideas for Bioinformatics Software Projects
capn_primer
Designs and validates primers, sails the seven seas.
fasta_length
Generates sequence length histogram from several fastas
FastaLocTable
Writes a table of fasta sequence bases at locations
loci_translate
Translates loci using an .agp file
MoanaPipelines
Pipelines to analyze and correct reads, count kmers and assemble genomes -- meant to run on our local cluster
no_bad_products
Cleans up annotation syntax to conform to NCBI standards
ped_tools
Tools to tweak and validate and reformat PED files
PySTACKS
Python STACKS pipeline
reformat
Tool that outputs structure and pedegree files from .vcf, plink.map, plink.ped, hapmap files
seq_coverage
Calculates coverage of sequence across fasta files
taskmaker
Helper program to create SGE job scripts
WhosYourDaddy
A simple tool to find a Father's genome if it has gone missing
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