Archana Malhotra
Computational Biologist
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NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1927 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2657 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...Staff Scientists at National Institute of Plant Genome Research, New Delhi
National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The...BBTools for bioinformatician !
By Surabhi Chaudhary 2616 days ago Comments (1)BBTools can do almost everything now !AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2443 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...AMStat: display statistics of large sequence files from next generation sequencing projects
By Neel 2349 days agosamstat.sourceforge.net - SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads...Understanding HiFi Reads !
By Rahul Nayak 1118 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 1941 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2534 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...
