Jit
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lsugenomics Lab
In our lab, we seek to characterize and to compare genomes in order to better understand genetic and evolutionary processes linking genotypes to phenotypes. Sequencing and decoding plant genomes have been integral in our approaches. The...Proksee
By LEGE 240 days agohttps://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file. Please Cite the Following Grant JR, Enns E, Marinier E,...Metassembler: merging and optimizing de novo genome assemblies
By Rahul Nayak 2390 days agosourceforge.net - Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2241 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2199 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1598 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...HALC: High throughput algorithm for long read error correction
By Jit 2359 days ago Comments (1)github.com - HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...Shasta long read assembler
By Jit 1774 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 2453 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2383 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...
