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LRCstats: a tool for evaluating long reads correction methods
By Aaryan Lokwani 2912 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 2959 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...ONT assembly and Illumina polishing pipeline
By Jit 3184 days agogithub.com - This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous steps...dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
By Rahul Nayak 3175 days agogithub.com - dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...Ra assembler - a de novo DNA assembler for third generation sequencing data
By biogeek 3150 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...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 3039 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...EAGLER: a scaffolding tool for long reads.
By Jit 2991 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...SWALO: Scaffolding with assembly likelihood optimization
By Jit 2975 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...Converting a VCF into a FASTA given some reference !
By Jit 2945 days agoconverting a VCF file into a FASTA file given a reference sequenceLong read assembly workshop !
By Rahul Nayak 2869 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...
