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ChakrabortyLab's Projects

assembly-error icon assembly-error

Methods and notes on how to detect assembly errors in long molecule based assemblies

dedup icon dedup

Separates redundant contigs from an assembly

diploid-asm icon diploid-asm

Contains prototype scripts for diploid assembly of long reads

dspr-asm icon dspr-asm

Contains scripts and programs used to generate assemblies and variants for the DSPR project

dspr-popgen icon dspr-popgen

Contains programs and scripts for the dspr popgen project

falcon_unzip icon falcon_unzip

Making diploid assembly becomes common practice for genomic study

mito-finder icon mito-finder

Assembling mitochondrial genomes from long molecule sequences

mlift icon mlift

A mummer based genomic coordinate liftover tool

mplotter icon mplotter

Creates publication quality dot plot using ggplot

proberead icon proberead

A light weight utility program to extract reads that span genomic intervals

quickmerge icon quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

sim-complex icon sim-complex

Contains assemblies and scripts relevant to the sim-complex paper

stephensi_genome icon stephensi_genome

Contains scripts and detailed methods used for making figures and data analysis

svmu icon svmu

A program to call variants from genome alignment

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