skingan
Bioinformatics Scientist in Applications at PacBio. Genome assembly, dataQC for novel library prep, long reads.
@PacificBiosciences Menlo Park, CA
Pinned Repositories
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
CSC162
Collection of python scripts for Data Structures and Algorithms course
FC_Unzip_HaplotypeDivergence
summarize haplotype divergence in unzipped regions
HomolContigsByAnnotation
python script to identify genes that are present on multiple contigs
NCBI_DiploidAssembly
scripts to generate files associated with NCBI submission of diploid genome assembly
purge_haplotigs_multiBAM
branch of purge haplotigs that inputs multiple bam files
score_phase
snakemake tool for scoring haplotype phase in diploid assemblies
sim-low-input
Simulate PacBio Low Input HiFi Reads
skingan's Repositories
skingan/purge_haplotigs_multiBAM
branch of purge haplotigs that inputs multiple bam files
skingan/adapt_PurgeHaplotigs_for_FALCONPhase
Convert output of purge haplotigs to format compatible with FALCON-Phase
skingan/HomolContigsByAnnotation
python script to identify genes that are present on multiple contigs
skingan/NCBI_DiploidAssembly
scripts to generate files associated with NCBI submission of diploid genome assembly
skingan/AaegL5_FinalPolish
data files and scripts used for final polishing of scaffolded, gap-filled assembly
skingan/CDS2SFS
Calculates site frequency spectra for synonymous and nonsynonymous sites in coding sequence alignment
skingan/CSC162
Collection of python scripts for Data Structures and Algorithms course
skingan/FC_Unzip_HaplotypeDivergence
summarize haplotype divergence in unzipped regions
skingan/score_phase
snakemake tool for scoring haplotype phase in diploid assemblies
skingan/sim-low-input
Simulate PacBio Low Input HiFi Reads
skingan/CDSgffSNP2fa
A perl script to generate fasta sequences for coding regions specified in gff file.
skingan/combineSNPfiles
A perl script to merge multiple files created by POPBAM SNP into a single file.
skingan/dna_functions
a few functions for kmer counting and random sequence generation
skingan/FP_validation
scripts for testing FALCON-Phase results against TrioCanu assemblies
skingan/gc_cov_2
skingan/gc_cov_snake
tool for generating coverage by gc plots
skingan/HaplotigPlacement
skingan/JammerStats
An R function for calculating total points and lead jam percentage
skingan/mauGenome_v2_Orthologs
python script to convert gene IDs between genome versions
skingan/MHC_KIR
tools to assess PacBio performance in de novo assembly of challenging regions
skingan/NCBI_human_assembly_stats
skingan/PBsnp2fa.pl
Convert POPBAM SNP output to fasta sequence
skingan/purge_dups
skingan/removeNestedHaplotigs
A tool for removing nested haplotigs from a FALCON-unzip assembly
skingan/SBKingan_Resume
skingan/simulansCladeMIR
Suite of python scripts to generate species-specific miRNA sequences in Drosophila simulans clade
skingan/TrioBinning
Scripts for manually classifying reads and make figures