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scripts

00_pangenome_analysis

Pangenome Analysis Workflow with Prodigal and CD-HIT

12-trees

Variants analysis

a188ref1

the process to build the first A188 reference genome

ab10-assembly

B73Ab10 genome assembly methods

adapt_purgehaplotigs_for_falconphase

Convert output of purge haplotigs to format compatible with FALCON-Phase

adaptiphy

This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"

admixturepipeline

A pipeline that accepts a VCF file to run through Admixture

adratio

Classifying sex-linked and autosomal scaffolds using allele-depth ratios computed from pileup data

ak47

product for bioinfo

aldy

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

aligngraph2

Similar genome assisted reassembly pipeline for PacBio long reads

alignwise

allele-biased-expression

Guide to uncover parent-of-origin gene expression bias

allele-specific-expression

Pipeline to perform the allele-specific expression analysis developed by Skelly et al. (2011) on phased data.

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

allis

Allele-specific expression

alpha-centauri

A python package from Pacific Biosciences to analyze centromeric sequences

amphioxusgenome

ampril-genomes

scripts for the project of seven thaliana genomes assembly

ancestral-blocks-reconstruction

ancestral_genome_reconstruction

Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO

ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

anges

Reconstruction of ancestral genome maps

annotation

Scripts used in the annotation of B10K genomes

anole_expression

Understanding variation in squamate sex determination and sex chromosome evolution

aphid_al4_chromosome_assembly

The analytical pipeline of the AL4 strain genome

apps-scripts

Miscellaneous scripts for applications of PacBio systems

aquila

Diploid personal genome assembly and comprehensive variant detection based on linked-reads

arachis