Plastid Genome Annotator

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

MFannot is a program for the annotation of mitochondrial and plastid genomes

Merge transcriptome read-to-genome alignments into non-redundant transcript models

Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

parallelLastz: Running Lastz in parallel

Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories

QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organism Genomes to Advance Comparative Genomics

Targeted Amplicon Bisulfite Sequencing Analysis Tool

Software for creating and comparing genome fingerprints.

Copy number estimation of highly duplicated sequences

Organelle Genome Assembler

Automated pipeline for HGT and contaminant detection in an assembled, annotated genome

A computational toolkit of fast and automatical identification of back-splice junctions of potential circular RNAs (circRNAs) from RNA-seq data.

A repository for scripts used in genome project ➡ https://tiramisutes.github.io/Genome_Scripts/

get chloroplast and mitochondrial genes from contigs of genome-skimming or transcriptome data

A utility to call polyA sites based on genome alignments in SAM format

This is the github repository for the Eichler lab Amazon Web Services (AWS) pipelines