Archana Malhotra
Computational Biologist
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A 3D Map of the Human Genome
By Jitendra Narayan 3680 days agoSuhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand,...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1711 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...
Short-read assembly using Spades !
Last updated 1074 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...Phased Human Genome Assembly !
By Rahul Nayak 2285 days agoDiploid Assembly of a Puerto Rican Female Adds a Rich Resource to Population-Specific Reference GenomesCerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2410 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2317 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Sequencing By Xpansion
By Jitendra Narayan 3493 days agoXpandomer in a single drop reaction to sequence an entire human genome 1000X over.Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2417 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...Genome Stability Laboratory
The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p,...MAKER
By Jitendra Narayan 3259 days ago Comments (1)www.yandell-lab.org - MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats,...
