Pontus Höjer's repositories
awesome-linked-reads
Collection of tools and resources for linked-reads
Aquila
Diploid personal genome assembly and comprehensive variant detection based on linked-reads
bioconda-recipes
Conda recipes for the bioconda channel.
CheckConstruct
Check PCR constructs
Clew
Handling of ChIB data
cue
Deep learning framework for SV calling and genotyping
ema
Fast & accurate alignment of barcoded short-reads
flyttdata
Flyttdata
genetech
material related to the genetech courses
HapCUT2
software tools for haplotype assembly from sequence data
LRez
Standalone tool and library allowing to work with barcoded linked-reads
misc
Collection of useful scripts
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
Novel-X
Novel insertion detection with 10X reads
planets-phojer
Programming Formalisms course HT 2023
pontushojer
About me
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.
samplot
Plot structural variant signals from many BAMs and CRAMs
scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
starcode
All pairs search and sequence clustering
whatshap
Read-based phasing of genomic variants, also called haplotype assembly