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formicidaemolecularevolution

Scripts and how-tos for comparative genomics work.

four-fold_degenerate_bedmaker

A python script to identify four-fold degenerate sites from a CDS fasta

gaap

A genome assembly assessment pipeline.

gce

GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.

genome-annotation-pipeline

Genome annotation pipeline

genome_assembly_assessment

genomeassemblytools

A collection of scripts I use in genome assembly

ggcor

Extended tools for correlation analysis and visualization.

gitskill

go_kegg_annotation

GO KEGG annotation

googletranslateipcheck

hi-c-scaffolding-pipelines

I'm sharing my automation of the 3D_DNA and SALSA Hi-C scaffolding pipelines.

hic_scripts

HiC processing scripts used in the center.

hic_tools

A collection of tools for Hi-C data analysis

hicassembly

Pipeline using HiC data to help the genome assembly

icca

We propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs.

jaltgenome

Raw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.

kmer-based-subgenome-mapping

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

learngit

libyaml

Canonical source repository for LibYAML

long-read-pipelines

Long read production pipelines

long_read_genome_assembly

A shell script I wrote while exploring long read genome assembly tools. In this script assembly is done using an example ONT fastq read data and uses shasta, canu, Flye, Miniasm and wtdbg2. The script compares the assembly statistics using QUAST.

longrepmarker_v2.0

ltr-insertion-time-estimation

masurca

mepmodeler

Predict MicroExons in Plant Genomes

multispecies_hic

Multi-species pipeline for Hi-C data

my_scripts

myscripts