Jit
Enthusiast computational biologist with business dream !!!
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PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3209 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...MUMmer4: A fast and versatile genome alignment system
By Jit 3145 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...WhatsHap: fast and accurate read-based phasing
By Jit 3031 days agowhatshap.readthedocs.io - WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2627 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 762 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...Kaiju
By Jit 3731 days agohttp://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...Tiara: deep learning-based classification system for eukaryotic sequences
By Rahul Nayak 1644 days agoacademic.oup.com - With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 3201 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...Ancestral sequence reconstruction (ASR) or ancestral gene/sequence reconstruction/resurrection...
By Jit 3394 days ago Comments (2)Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolutionPANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the...
By BioStar 2915 days agogithub.com - Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via: sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config On MacOS, the Apple...
