Rahul Agarwal
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INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2553 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...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 2522 days agogithub.com - Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2395 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2384 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2357 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2301 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2278 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...d2Tools: The toolbox for counting the frequency of k-tuple from sequencing datasets and calculate...
By Jit 2256 days agocode.google.com - d2Tools are the toolbox for counting the frequency of K-tuple from sequencing datasets and then calculating the pairwise dissimilarity matrix between samples with the d2-style(d2/d2*/d2S representing d2/d2Star/d2shepp, respectively)...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2188 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2132 days agogithub.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...
