Pinned Repositories
assannphy
Assembly, Annotation, and Phylogenetics of bacterial genomes
bredeson.github.io
DBG2OLC
The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
Dioscorea-alata-genomics
Code and data from the Bredeson, Lyons, et al. Dioscorea alata var. TDa95/00328 v2 genome and analysis manuscript.
EIG
Eigen tools by Nick Patterson and Alkes Price lab
HandsOnDArT
Hands-on analysis of DArTseq data for linkage mapping
merqury
k-mer based assembly evaluation
pfb2022
Programming for Biology Class @ CSHL 2022
pfb2024
Programming for Biology @ CSHL 2024
bifrost
Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
bredeson's Repositories
bredeson/Dioscorea-alata-genomics
Code and data from the Bredeson, Lyons, et al. Dioscorea alata var. TDa95/00328 v2 genome and analysis manuscript.
bredeson/pfb2022
Programming for Biology Class @ CSHL 2022
bredeson/HandsOnDArT
Hands-on analysis of DArTseq data for linkage mapping
bredeson/assannphy
Assembly, Annotation, and Phylogenetics of bacterial genomes
bredeson/bredeson.github.io
bredeson/DBG2OLC
The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
bredeson/EIG
Eigen tools by Nick Patterson and Alkes Price lab
bredeson/merqury
k-mer based assembly evaluation
bredeson/PFB2012
Code and samples from lecture and review sessions
bredeson/pfb2017
bredeson/pfb2024
Programming for Biology @ CSHL 2024
bredeson/pfb2018
bredeson/PFB2018-final-project
Protein evolution and annotation project
bredeson/pfb2019
Programming for Biology 2019
bredeson/pfb2023
Programming for Biology @ CSHL 2023
bredeson/PnP
Prisons and Python
bredeson/snp
SNP software to analyze and annotate variant files
bredeson/STARalign
Pipeline to align RNA-seq reads to a genome using STAR with splice junctions