Rahul Nayak
A Bioinformatician
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My commonly used commands in Bioinformatics
Last updated 2312 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta...Referee: Genome assembly quality scores
By Jit 2210 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...ngs-bits - Short-read sequencing tools
By Neel 1772 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for WindowsUnderstanding your reads and mapping !
By Neel 1760 days agobioinformatics-core-shared-training.github.io - One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.htmlPostdoctoral Researcher in Cancer Systems Biology
Postdoctoral Researcher in Cancer Systems Biology Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford Grade 7: £30,434 - £37,394 with a discretionary range to £40,847 p.a. Applications are invited for a Postdoctoral...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2552 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2399 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...-
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2383 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw... P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2356 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2269 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...
