Jit
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pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2844 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...How to sequence the human genome - Mark J. Kiel
By Rahul Nayak 4299 days agoView full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological...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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2531 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University
Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India"...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2223 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...dcGOR
By Martin Jones 4137 days agoan R package for analysing ontologies and protein domain annotationsSLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2213 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:ICGEB Bioinformatics RA/SRF/JRF Vacancies
Research Associate/JRF/SRF position, DBT Sponsored Bioinformatics Infrastructure Facility Applicants should hold a PhD or a first class MSc/MTech degree in Bioinformatics of Biotechnology/Life Sciences; experience in using bioinformatics tools,...KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina...
By Jit 2087 days agogithub.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...
