Resources

Software

Quickmerge

A meta-assembler that merges two assemblies created using long reads, or long reads and long+short reads. In reality it can merge any two sequences. That way, quickmerge can also be used to manually assemble ultra-long reads (as produced by Oxford nanopore). [link] Read more.

SVMU (Structural Variants from MUmmer)

SVMU can be used to identify all differences between two genomes. It annotates large scale structural differences, as well as small indels and SNPs. [link] Read more.

mscaffolder

A comparative genome assembly scaffolding tool. It scaffolds contigs of one assembly based on another. Often, running mscaffolder on a assembly prior to running SVMU is helpful. [link] Read more.

mlift

mlift is genomic coordinate liftover tool based on MUMmer. It can lift coordinates of sequence features that span as little as 1 nucleotide. [link] Read more.

Materials

Research in the Chakraborty lab often requires development of new experimental resources (e.g. transgenic Drosophila). This is a list of materials that we have developed and are available upon request.

Aldh-RFP

A Drosophila strain carrying a RFP tagged Aldehyde dehydrogenase gene and a GFP gene tagged with mitochondrial leader peptide. Both ALDH-RFP and mito-GFP colocalize, showing the mitochondrial localization of ALDH. Read more.

Data

All genome, pangenome, and relevant databases are available here.

Drosophila Laboratory Pangenome Database (DLPD)

Since T.H. Morgan and his associates in the famous Fly Room began their foundational work in genetics using the mighty fruit fly Drosophila melanogaster, numerous strains of Drosophila have been created in laboratories worldwide. These include transgenic strains, deficiency strains, RNAi, genome editing, and balancers, as well as wild-type strains (e.g., Oregon-R, w1118, Canton-S). The genetic background of these strains differs from the reference strain ISO1 and remains unknown. These uncharacterized differences confound the interpretation of experiments investigating the genotype-phenotype relationship using these non-reference laboratory strains. To solve this problem, we introduce the Drosophila Laboratory Pangenome Database (DLPD), a collection of ever-growing reference genome assemblies of popular D. melanogaster strains. Although twelve genome assemblies will be released initially, more will be added in the future (depending on the feedback from the community). We are in the final stage of setting up a genome browser for easy access to this data and will provide a link to the browser and the full dataset here. Stay tuned! Read more.

All of our software and materials are free (unless otherwise noted). Over the last 20 years, Mahul benefited from public schools in various stages of his education so this is one tiny way he can say thank you to all the taxpayers in India and USA. However, if any of the software or materials mentioned here has benefited your research, we invite you to make a donation to Pratyush, an NGO in India, in which Mahul is actively involved. Pratyush is engaged in improving the lives of under-privileged children and women using a holistic approach.

Donate to Pratyush

Quickmerge

SVMU (Structural Variants from MUmmer)

mscaffolder

mlift

Contact