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SPADes team announce new version SPADes v3.15
By BioStar 1877 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamGenome Assembly Workshop 2020
By Jit 1656 days agoucdavis-bioinformatics-training.github.io - Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when...ALE: Assembly Likelihood Estimator
By BioStar 1096 days agogithub.com - Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 637 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2827 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...LoRDEC: a hybrid error correction program for long, PacBio reads
By Jit 3254 days agowww.atgc-montpellier.fr - LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read...LRCstats: Long Read Correction Statistics
By Jit 2984 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...HALC: High throughput algorithm for long read error correction
By Jit 2830 days ago Comments (1)github.com - HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2754 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2802 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...
