Key Education Issues in Review: Nevada Academic Content Standards

final_soap_GNV120025.fa: Assembly of Hemiargus ceraunus from Genbank SRA accession #SRR1299274, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Kawahara and Breinholt (2014) for more details

Scripts_README

Description of the python scripts and direction how to run them

removelist

python script to remove list of sequences from a fasta fil

contamination_filter

python script to process blast results of blasting sequences from each loci against themselves using usearch to identify contaminatio

hema2_assembly

hema2_assembl

SOAP_assembly.qsub

This script was used for multiple kmer transcriptome assemblies. The script is specific to the University of Florida module system but can be easily edited for use on other HPC systems

split

python script to split a single line fasta file with many loci into locus specific fasta file

alignment_DE_trim

python script to trim alignments by density and entrop

extract_probe_region

python script to split alignment into head, probe, and tail regions based on the beginning and end of a reference sequence in the alignmen

Taxon_list.txt

List of taxa codes and names and source of data for the two nexus files below in tab-delimited text