Jit
Enthusiast computational biologist with business dream !!!
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Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
By Jit 3132 days agobioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...Edanchin Lab
My main topics of interest are: The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology Evolution and adaptation of animals in the absence of sexual reproduction and the underlying...PRISM
By Jit 2904 days agocompbio.cs.toronto.edu - PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with...Next Generation Sequencing (NGS) Tutorials
By Jitendra Narayan 4109 days ago Comments (31)chagall.med.cornell.edu - Institute of computational biomedicine, Cornell University provide an NGS workshop tutorial at http://chagall.med.cornell.edu/NGScourse/ You can also add your favourite NGS educational material, or workshop tutorial by commenting on this...TEannot
By Jit 3018 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2168 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Environmental Genomics Group SciLifeLab/KTH Stockholm
By BioStar 723 days agohttps://github.com/envgen - Useful Metagenomics resourcesVariant Calling Pipeline
By LEGE 34 days agogithub.com - The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the...Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
By Jit 2556 days agosourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...PGAP-X: Extension on pan-genome analysis pipeline
By Rahul Nayak 2495 days agohttps://pgapx.ybzhao.com/ - PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...
