Rahul Agarwal
I'm a Bioinformatician and Programmer
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NanoPack: visualizing and processing long-read sequencing data
By Jit 2158 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2061 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 1835 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1760 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1639 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1001 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Illumina Smartphone Chip !!!
By Robert M Willioms 3614 days agoIllumina, the company that claims it brought human genome sequencing down to $1000 prices, has now turned its attention to a consumer product - a chip that you can plug into your smartphone and have it read your genetic information.Trimmomatic: A flexible read trimming tool for Illumina NGS data
By Jit 3143 days agowww.usadellab.org - Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10...QuorUM: An Error Corrector for Illumina Reads
By Jit 2571 days agojournals.plos.org - Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...Illumina to Acquire Pacific Biosciences for Approximately $1.2 Billion !
By Rahul Nayak 2212 days agohttps://www.illumina.com/company/news-center/press-releases/2018/2374913.html
