Jit
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SvABA: Genome-wide detection of structural variants and indels by local assembly
By Abhimanyu Singh 2111 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....Prof. Dr. rer. nat. Jeanette Erdmann's Lab
Category: researchlabs:Bioinformatics
PI: Prof. Dr. rer. nat. Jeanette Erdmann
By Rahul Agarwal 2511 days agoHer prestigious lab working on Integrative and Experimental genomics to understand the underlying mechanism thats able to define an inherited predisposition of coronary artery disease (CAD) and myocardial infarction (MI) via GWAS, different...MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...
By Jit 2516 days ago Comments (1)github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2362 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2198 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...How to sequence the human genome - Mark J. Kiel
By Rahul Nayak 3808 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...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3087 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...TMAP - torrent mapping alignment program General Notes
By Poonam Mahapatra 2770 days agogithub.com - TMAP - torrent mapping alignment program General Notes TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies. The latest TMAP is unsupported. To use a...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2265 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....Protein function annotation and machine learning - UPMC - Paris, France
Protein function annotation and machine learning - UPMC - Paris, France Job Description: We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open...
