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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 days ago): Sequencing coverage is defined as the average number of reads that covers...
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EFS: an ensemble feature selection tool implemented as R-package and web-application
By Jit 1761 days ago Comments (1)http://efs.heiderlab.de/ - The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in...mutatrix: a population genome simulator which generates simulated genomes.
By Jit 1761 days agogithub.com - genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fastaGlia: a Graph/Smith-Waterman (partial order) aligner/realigner
By Jit 1761 days agogithub.com - glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f...VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 1761 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1761 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtMALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
By Jit 1761 days agogithub.com - MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being...Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
By Jit 1761 days agogithub.com - Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 1761 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 1761 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...Genome in a Bottle (GIAB) Consortium
By Jit 1763 days ago Comments (3)jimb.stanford.edu - The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome...
