Poonam Mahapatra
Bioinformatics Researcher
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Tools to access the quality of your assembled genome !
Last updated 790 days ago by LEGEFASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...Step-by-Step Guide to Running Genome Assembly
By Abhi 663 days agoGenome assembly is a powerful process that transforms raw sequencing data into a coherent representation of an organism’s genome. By following this step-by-step guide, you can successfully assemble genomes and uncover valuable biological insights....Genomic architecture surrounding the fusion site of human chromosome 2
By LEGE 582 days agoThis fusion event is a key evolutionary marker distinguishing humans from other great apes, as humans have 46 chromosomes while chimpanzees, gorillas, and orangutans possess 48. The fusion occurred through an end-to-end joining of two ancestral...A Subway Map for the Genome
By LEGE 33 days agoInstead of showing a genome as one long, confusing sequence, it displays different genomic paths like routes on a metro map. Where sequences are shared, the paths travel together. Where genetic variation occurs, they branch into different routes...The Genes That Travel Together: A Genomic Detective Story
By BioStar 26 days agoImagine looking through thousands of microbial genomes and discovering two genes that repeatedly appear together. The obvious conclusion is that they must somehow be connected—that perhaps they work together, participate in the same pathway, or...GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3409 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...-
Run miniasm assembler on nanopore reads !
Last updated 3215 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream... minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 3058 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 3046 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...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2983 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...
