Abhimanyu Singh
A bioinformatics beginner
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Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 3039 days agogithub.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2826 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2835 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...A guide to machine learning for biologists
By LEGE 1634 days agowww.nature.com - We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to...Powerful books for learning data analysis with R
By LEGE 648 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...LAMSA: fast split read alignment with long approximate matches
By Jit 2853 days ago Comments (1)github.com - LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the...nanofilt: Filtering and trimming of long read sequencing data
By Jit 2777 days ago Comments (1)github.com - Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2722 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Shasta long read assembler
By Jit 2244 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...
