Neel
Bioinformatics Beginner
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By Jit 2829 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for BioinformaticsP_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
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By Jit 2756 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....Long read assembly workshop !
By Rahul Nayak 2711 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...Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
By BioStar 2672 days agogithub.com - Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source...
Evaluation of genome assembly software based on long reads
By BioStar 2591 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact...
By Neel 2267 days agogithub.com - Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2222 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
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