Abhimanyu Singh
A bioinformatics beginner
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LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2738 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2766 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 1951 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesTAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2852 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 1816 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...DMINDA2: an integrated web server for DNA motif identification and analyses
By BioStar 2224 days agobmbl.sdstate.edu - DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses More at http://bmbl.sdstate.edu/DMINDA2/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/fastv - detect virus
By Jit 1546 days agogithub.com - fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect...geNomad: Identification of mobile genetic elements
By LEGE 187 days agoportal.nersc.gov - geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 3208 days agosourceforge.net - Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,...LRCstats: Long Read Correction Statistics
By Jit 2982 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...
