Stars
Code and data to reproduce results from Ruegg et al. paper on the Willow Flycatcher genoscape
A course on genomics and bioinformatics from WU
Resources for Brown University's BIOL 1435 course.
Foreign Contamination Screening caller scripts and documentation
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.
asl / BandageNG
Forked from rrwick/Bandagea Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Graphical Fragment Assembly (GFA) Format Specification
Annotation helper tool for the manual curation of transposable element consensus sequences
Extracts records from a fasta based on a list of fasta headers.
Visualizing transcript structure and annotation using ggplot2
A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
molikd / HiFiAdapterFilt
Forked from sheinasim/HiFiAdapterFiltConvert .bam to .fastq and remove reads with remnant PacBio adapter sequences
DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
scaffolding based on Hi-C, 10X linked reads, linkage disequilibrium information.
A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotator (EDTA), DeepTE, RepeatMasker and RM_TRIPS.
Test sets and pipeline scripts for pan-genomic graph analysis