Aaryan Lokwani
A Bioinformatician
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QuorUM: An Error Corrector for Illumina Reads
By Jit 3139 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...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2720 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
By BioStar 2697 days agogithub.com - NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2832 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 2055 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....FiNGS: Filters for Next Generation Sequencing
By Neel 1932 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...1mb long DNA with Nanopore technology
By Jit 3098 days agoLongest read of 1mb achievements with NanoporeNanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 3099 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2966 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...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2943 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...
