kfwins2022's Projects
Rapid large-scale prokaryote pan genome analysis
Wrapper R scripts for performing a weighted-gene co-expression network analysis (WGCNA)
Novel Discovery of Phages from Salmonella Sequences
Filter SAM file for soft and hard clipped alignments
Pan-genome wide association studies
An R package for simulating RNA-sequence datasets from regulatory networks
Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
SeqSero2
โกโ ๏ธ Assemble bacterial isolate genomes from Illumina paired-end reads
A fast whole-genome aligner based on de Bruijn graphs
HMM-HDP models for MinION signal alignments (not mine, just collecting it for my pipelines)
SNP and variant calling pipeline for bacteria
SPAdes Genome Assembler
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
A tool for generating consensus long-read assemblies for bacterial genomes
Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks
In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!
hybrid assembly pipeline for bacterial genomes