Rahul Nayak
A Bioinformatician
Our Sponsors
Related items
Carefully opt for human reference genome
By biogeek 1739 days agolh3.github.io - Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the...EAGLER: a scaffolding tool for long reads.
By Jit 2364 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...
Download blasr 1.3 version
By Jit 2353 days agoDOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error: fail to open file './temporarySam' [bwa_aln_core] write to the...Converting a VCF into a FASTA given some reference !
By Jit 2317 days agoconverting a VCF file into a FASTA file given a reference sequenceLR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
By Rahul Nayak 1653 days agogithub.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...Long read assembly workshop !
By Rahul Nayak 2241 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2201 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...Versatile genome assembly evaluation with QUAST-LG
By Jit 2163 days agocab.spbu.ru - QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST package starting from version 5.0.0 (download the latest release). Run QUAST as...LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
By Neel 2140 days agogithub.com - LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then...CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS...
By BioJoker 2054 days agowww.nature.com - Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975
