Pinned Repositories
bioperl-run
BioPerl wrappers
bredeson.github.io
bz2file
Python library for reading and writing bzip2-compressed files.
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
FALCON
FALCON: experimental PacBio diploid assembler
HandsOnDArT
Hands-on analysis of DArTseq data for linkage mapping
merqury
k-mer based assembly evaluation
pfb2022
Programming for Biology Class @ CSHL 2022
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/bioperl-run
BioPerl wrappers
bredeson/bredeson.github.io
bredeson/bz2file
Python library for reading and writing bzip2-compressed files.
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/FALCON
FALCON: experimental PacBio diploid assembler
bredeson/merqury
k-mer based assembly evaluation
bredeson/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bredeson/PFB2012
Code and samples from lecture and review sessions
bredeson/pfb2017
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/pypeFLOW
a simple lightweight workflow engine for data analysis scripting
bredeson/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
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