douglasgscofield / PacBio-utilities
Collection of utilities for working with PacBio-based assemblies
☆13Updated last year
Related projects: ⓘ
- Python HyPhy: Facilitating HyPhy execution and parsing☆21Updated 2 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 5 years ago
- Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler☆15Updated 2 months ago
- WGS (Wheat) Robust Assembly Pipeline☆22Updated 3 years ago
- ☆12Updated 3 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆19Updated 8 years ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆38Updated 4 years ago
- A tool to extract LOH blocks from VCF, BAM and FASTA data☆20Updated 3 weeks ago
- Output FASTQ summary statistics in JSON format☆29Updated last year
- Annotated Genome Optimization Using Transcriptome Information☆20Updated 4 years ago
- Assembly by Reduced Complexity (ARC)☆41Updated 8 years ago
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆20Updated 7 years ago
- Find Unique genomic Regions☆29Updated 2 weeks ago
- NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore tech…☆15Updated 7 years ago
- Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …☆46Updated 2 years ago
- Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database☆10Updated 7 years ago
- Advanced metagenomic Sequence Analysis in R☆15Updated 6 years ago
- ☆18Updated last month
- Exact Tandem Repeat Finder (not a TRF replacement)☆45Updated 4 years ago
- transposable element typing pipeline☆15Updated 6 months ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Updated 6 years ago
- Validate and edit small eukaryotic genome assemblies☆31Updated last year
- Identifying repeats in high-throughput sequencing data☆15Updated 5 months ago
- OrthoFiller: Identifying missing annotations for evolutionarily conserved genes.☆22Updated last year
- Algorithm to divide a phylogenetic tree into segments based on phenotypes at the leaves of the tree☆25Updated 6 years ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Updated 5 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 2 years ago
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Updated 6 years ago
- PoSeiDon: positive selection detection and recombination analysis pipeline☆35Updated 2 years ago
- Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment☆21Updated last month