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aaegl5_finalpolish

data files and scripts used for final polishing of scaffolded, gap-filled assembly

adapt_purgehaplotigs_for_falconphase

Convert output of purge haplotigs to format compatible with FALCON-Phase

cds2sfs

Calculates site frequency spectra for synonymous and nonsynonymous sites in coding sequence alignment

cdsgffsnp2fa

A perl script to generate fasta sequences for coding regions specified in gff file.

combinesnpfiles

A perl script to merge multiple files created by POPBAM SNP into a single file.

csc162

Collection of python scripts for Data Structures and Algorithms course

dna_functions

a few functions for kmer counting and random sequence generation

fc_unzip_haplotypedivergence

summarize haplotype divergence in unzipped regions

fp_validation

scripts for testing FALCON-Phase results against TrioCanu assemblies

gc_cov_2

gc_cov_snake

tool for generating coverage by gc plots

haplotigplacement

homolcontigsbyannotation

python script to identify genes that are present on multiple contigs

jammerstats

An R function for calculating total points and lead jam percentage

maugenome_v2_orthologs

python script to convert gene IDs between genome versions

mhc_kir

tools to assess PacBio performance in de novo assembly of challenging regions

ncbi_diploidassembly

scripts to generate files associated with NCBI submission of diploid genome assembly

ncbi_human_assembly_stats

pbsnp2fa.pl

Convert POPBAM SNP output to fasta sequence

purge_dups

purge_haplotigs_multibam

branch of purge haplotigs that inputs multiple bam files

removenestedhaplotigs

A tool for removing nested haplotigs from a FALCON-unzip assembly

sbkingan_resume

score_phase

snakemake tool for scoring haplotype phase in diploid assemblies

sim-low-input

Simulate PacBio Low Input HiFi Reads

simulansclademir

Suite of python scripts to generate species-specific miRNA sequences in Drosophila simulans clade

triobinning

Scripts for manually classifying reads and make figures