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454_data_scripts

Useful code for parsing 454 data in FORTRAN

agp_tweaker

An amazing lil' Python utility to shift boundaries between given scaffold-contigs and fragments in an .agp file

annie

annie = ANNotation Information Extractor

bioinformatics-tools

Awk, bash, python scripts for processing NGS data

biosoftnamegen

Generates Amazing Ideas for Bioinformatics Software Projects

capn_primer

Designs and validates primers, sails the seven seas.

contigger

Splits your scaffolded fasta into contigs and produces a gap file for use with GAA

fasta_length

Generates sequence length histogram from several fastas

fastaloctable

Writes a table of fasta sequence bases at locations

gag

Generates an NCBI .tbl file of annotations on a genome.

genomeannotation.github.io

hamstrfiltr

Start with a genome, single copy orthologs and SNPs; end with a list of the SNPpiest single copy ortholog exons in the genome

heatmap

Generates a heat map from a matrix of numbers

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

name_change

Tool to rename a list of names in a file from a provided dictionary file

no_bad_products

Cleans up annotation syntax to conform to NCBI standards

orthomcl-docker

An OrthoMCL setup in a docker image

ped_tools

Tools to tweak and validate and reformat PED files

phred

Translates Phred scores from ASCII to int and back again :)

pileup_analyzer

Python program to do wizardly stuff to samtools mpileup output

pylep_map

Python Bioinformatics pipeline for Lep-MAP, rQTL, Super-scaffold assemblies

pystacks

Python STACKS pipeline

reformat

Tool that outputs structure and pedegree files from .vcf, plink.map, plink.ped, hapmap files

scaffoldstoscaffoldcontigs

Command line Java tool to map a scaffolded genome to a scaffold-contigged version

seq_coverage

Calculates coverage of sequence across fasta files

snp_explorer

Console-based Python program for filtering vcf files

taskmaker

Helper program to create SGE job scripts

transvestigator

Validates transcriptome and prepares it for submission to the NCBI

unigener