Jit
Enthusiast computational biologist with business dream !!!
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McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 2110 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 688 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...SOAP2 : Short Oligonucleotide Analysis Package 2
By Poonam Mahapatra 2997 days agosoap.genomics.org.cn - SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2984 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...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2756 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
By Rahul Nayak 2356 days agoMCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal...Best Practices for Variant Calling with the GATK
By biogeek 2357 days agowww.broadinstitute.org - The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version...Kaiju
By Jit 3692 days agohttp://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...Rules for Pango Lineage !
By Abhi 1696 days agowww.pango.network - All the rules to classify a Lineage ! https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/CLARK: Fast, accurate and versatile sequence classification system
By Jit 2364 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...
