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anastrepha_ludens_genome_assembly

Scripts used to assemble the Anastrepha ludens genome

anastrepha_obliqua_genome_assembly

Scripts used to assemble the Anastrepha obliqua genome

blobblurb

Creates a tab-delimited summary blurb of BlobTools output.

bombus_huntii_genome_assembly

Scripts used to assemble the Bombus huntii genome

fastaparser

Extracts records from a fasta based on a list of fasta headers.

find_x_or_z

Use genotype data (biallelic SNP data in .vcf) to identify X or Z-linked scaffolds.

findcontaminantsfromblob

findduplicatesfrombusco

Identify duplicate contigs or scaffolds from BUSCO search. Contigs or scaffolds are identified as duplicates when they only contain duplicate BUSCOs and their removal does not impact the number of complete BUSCOs.

hifiadapterfilt

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

lachesis_assembly_formatter_for_tassel

lep-map_pipe

Pipeline for generating a linkage map and supporting files for QTL analysis

magic8ball

Python script that answers all of life's questions

mvmapper

mvMapper (Multivariate Mapper) is an interactive data exploration tool for multivariate analyses with associated geographic location information.

populationgenomicpipeline

Commands for performing a population genomic analysis from genome assembly to population genomic data visualization.

porexplorer

Visualize your raw Nanopore or PacBio sequences from fastq

seqer

Return .fasta containing records smaller than or larger than desired length.

sheinasim.github.io

sim_adapter_manuscript

Repository for commands and scripts used in data analysis for a manuscript

udownwithagp

Write NCBI .agp file from scaffold fasta

vim_lessons

Play with these text files and hone your vim skills

wxyandz_from_genotypes

Identify X/Z and Y/W linked-scaffolds from genotype heterozygosity and read depth data.

yacassf

Yet Another Contig and Scaffold Stat Finder