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Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2384 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 2335 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2270 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2150 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 1837 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...PhD position in Translational Medicine
https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca Essential experience / qualifications: Master /...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1428 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...The MARVEL assembler
By Jit 2395 days agogithub.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap...Cerulean: A hybrid assembly using high throughput short and long reads
By Rahul Nayak 2363 days agosourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4121 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
