Rahul Nayak
A Bioinformatician
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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...SPAdes
By Abhimanyu Singh 3609 days ago Comments (1)bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 3218 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2696 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 2133 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 3022 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...PAired-eND Assembler for DNA sequences
By Neel 3622 days agogithub.com - PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseqLACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2854 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1875 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1957 days agogithub.com - Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary...
