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Trinity RNA-Seq de novo transcriptome assembly
A curated list of awesome Perl frameworks and libraries. Come on Pull Requests!
✂️ ⚡ Rapid haploid variant calling and core genome alignment
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
MITObim - mitochondrial baiting and iterative mapping
Tools for working with second gen assemblies, fasta sequences, etc
Mapping pipeline for data generated using Arima-HiC
Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.
PacBio hybrid error correction through iterative short read consensus
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
Collection of scripts for bacterial genomics
Flexible circular visualization of genome-associated data with BioPerl and SVG.
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
TULIP - The Uncorrected Long read Itegration Pipeline
A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis
Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes
Wrapper scripts to run genome assembly scaffolding tools and scripts to analyse the output for accuracy.
Automated pipeline for HGT and contaminant detection in an assembled, annotated genome