Pinned Repositories
bacterial-genomics-tutorial
BEAVR
BEAVR: A Browser-based tool for the Exploration And Visualization of RNAseq data
canu
A single molecule sequence assembler for genomes large and small.
dotPlotly
Generate an interactive dot plot from mummer or minimap alignments
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
fastq-dl
Download FASTQ files from SRA or ENA repositories.
genomad
geNomad: Identification of mobile genetic elements
genotype_plot
A set of functions to visualise genotypes based on a VCF
ISEScan_stats
Condense and summarize many results form ISEScan into CSV for heatmaps
mGEMS
mGEMS Genomic epidemiology with mixed samples
gaworj's Repositories
gaworj/bacterial-genomics-tutorial
gaworj/BEAVR
BEAVR: A Browser-based tool for the Exploration And Visualization of RNAseq data
gaworj/canu
A single molecule sequence assembler for genomes large and small.
gaworj/dotPlotly
Generate an interactive dot plot from mummer or minimap alignments
gaworj/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
gaworj/fastq-dl
Download FASTQ files from SRA or ENA repositories.
gaworj/genomad
geNomad: Identification of mobile genetic elements
gaworj/genotype_plot
A set of functions to visualise genotypes based on a VCF
gaworj/ISEScan_stats
Condense and summarize many results form ISEScan into CSV for heatmaps
gaworj/mGEMS
mGEMS Genomic epidemiology with mixed samples
gaworj/MitoCode_R_Workshops
R markdown files which I have prepared for my work buddies at Ochota Campus in Warsaw,Poland as materials for the workshops aiming at teaching biologist the benefits of using R for data analysis
gaworj/nanopolish
Signal-level algorithms for MinION data
gaworj/NASQAR
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
gaworj/NGSpeciesID
Reference-free clustering and consensus forming of long-read amplicon sequencing
gaworj/ntEdit
✏️ultra fast and scalable genome assembly polishing
gaworj/pipits
Automated pipeline for analyses of fungal ITS from the Illumina
gaworj/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
gaworj/Sniffles
Structural variation caller using third generation sequencing
gaworj/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
gaworj/tormes
Making whole bacterial genome sequencing data analysis easy
gaworj/Unicycler
hybrid assembly pipeline for bacterial genomes
gaworj/unimap
A fork of minimap2 optimized for assembly-to-reference alignment
gaworj/useful-scripts
gaworj/utility
Useful bash one-liners for bioinformatics.