pgonzale60
Pipeline monkey at EPI2ME @nanoporetech. Also a genomicist for programmed DNA elimination.
Pinned Repositories
nxf_pipelines
Testing parallelization with nextflow
telomeric-trim
Get reads with telomeric repeat, trim the repeat and orient the trimmed end as the new beginning
testKal
Explore differences between Kallisto, HISAT2-featurecounts, HISAT2-stringtie. The results are benchmarked by assessing the sylamer enrichment signal. The datasets used involve miRNA abundance alterations.
vis_ALG
Visualize ancestral linkage groups by BUSCO in genome sequences (chromosomes)
pgonzale60's Repositories
pgonzale60/nxf_pipelines
Testing parallelization with nextflow
pgonzale60/telomeric-trim
Get reads with telomeric repeat, trim the repeat and orient the trimmed end as the new beginning
pgonzale60/testKal
Explore differences between Kallisto, HISAT2-featurecounts, HISAT2-stringtie. The results are benchmarked by assessing the sylamer enrichment signal. The datasets used involve miRNA abundance alterations.
pgonzale60/vis_ALG
Visualize ancestral linkage groups by BUSCO in genome sequences (chromosomes)
pgonzale60/bamregionextractor
Extract and count regions from BAM files as specified in BED, outputting as JSON and FASTA
pgonzale60/biocode
Bioinformatics code libraries and scripts
pgonzale60/busco2phylo-nf
Nextflow pipeline for turning a set of BUSCO results into a species tree
pgonzale60/caeno_synteny_comparison
pgonzale60/docker_images
A place to put Dockerfile for my Docker repositories
pgonzale60/genokmer_hifi
Reproducible genome size estimation from hifi reads
pgonzale60/nemADSQ
A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC
pgonzale60/Nonmodel-Species
Contains scripts used to annotate the genome assembly and compare alternative annotation approaches
pgonzale60/oscheius_drafts
draft Oscheius assemblies
pgonzale60/otipu_chrom_assem
Scripts and files associated with the chromosomal assembly of O. tipulae manuscript
pgonzale60/pgonzale60.github.io
Personal website
pgonzale60/samclip
Filter SAM file for soft and hard clipped alignments
pgonzale60/tandem_repeat_painting
Paint tandem repeats in chromosome level assemblies
pgonzale60/telomeric-identifier
Identify and find telomeres, or telomeric repeats in a genome.
pgonzale60/telomerTrimmer
Testing CI
pgonzale60/transcriptomic-exercise