Neel
Bioinformatics Beginner
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Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2953 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
By Jit 2944 days agoshendurelab.github.io - LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 2209 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...BBTools for bioinformatician !
By Surabhi Chaudhary 3032 days ago Comments (1)BBTools can do almost everything now !QuasR: Quantification and annotation of short reads in R
By Neel 1757 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3692 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...EAGLER: a scaffolding tool for long reads.
By Jit 2923 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...Converting a VCF into a FASTA given some reference !
By Jit 2877 days agoconverting a VCF file into a FASTA file given a reference sequenceLong read assembly workshop !
By Rahul Nayak 2801 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...wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
By BioStar 2678 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...
