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• • Surabhi Chaudhary@surabhi

  

  Surabhi Chaudhary bookmarked SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms 2418 days ago

  SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes). How does SEX-DETector...

  http://lbbe.univ-lyon1.fr/-SEX-DETector-.html?lang=eg
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra posted to the wire 2418 days ago

  10 PhD positions in Poland http://www.wb.uj.edu.pl/en_GB/studia/phd-biology/recruitment #Poland #PhD
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a page titled Run miniasm assembler on nanopore reads ! 2418 days ago

  Must read paper https://genome.cshlp.org/content/27/5/737.full
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a page titled Run miniasm assembler on nanopore reads ! 2418 days ago

  Here’s the quick and dirty of what was done: 1 Run minimap: This uses a pre-built set of defaults (the ava-pb in the code below) for analyzing PacBio data. Minimap only accepts two FASTQ files and you need to map your FASTQ file...
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity 2419 days ago

  The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...

  https://github.com/kdmurray91/kwip
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2419 days ago

  PacBio Sequencing and Its Applications https://www.sciencedirect.com/science/article/pii/S1672022915001345 #PacBio #Application #NGS
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked Porechop: tool for finding and removing adapters from Oxford Nanopore reads 2419 days ago

  Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...

  https://github.com/rrwick/Porechop
• • Jit@jit.aber

  

  Jit bookmarked WhatsHap: fast and accurate read-based phasing 2420 days ago

  WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...

  https://whatshap.readthedocs.io/en/latest/
• • Jit@jit.aber

  

  Jit bookmarked Manta: rapid detection of structural variants and indels for germline and cancer sequencing... 2420 days ago

  Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles...

  https://github.com/Illumina/manta
• • Jit@jit.aber

  

  Jit posted to the wire 2420 days ago

  LiftOver Howto http://genomewiki.ucsc.edu/index.php/LiftOver_Howto #LiftOver #HowTo
• • Jit@jit.aber

  

  Jit bookmarked GenomeMapper: Simultaneous alignment of short reads against multiple genomes 2423 days ago

  GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...

  http://1001genomes.org/software/genomemapper.html
• • Jit@jit.aber

  

  Jit bookmarked pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file 2424 days ago

  pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...

  https://github.com/PacificBiosciences/pbalign
• • Jit@jit.aber

  

  Jit bookmarked minialign: fast and accurate alignment tool for PacBio and Nanopore long reads 2424 days ago

  Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...

  https://github.com/ocxtal/minialign
• • Surabhi Chaudhary@surabhi

  

  Surabhi Chaudhary bookmarked %MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on... 2424 days ago

  %MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the...

  http://www.codons.org/
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra bookmarked SOAP2 : Short Oligonucleotide Analysis Package 2 2425 days ago

  SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of...

  http://soap.genomics.org.cn/soapaligner.html
• • Jit@jit.aber

  

  Jit posted to the wire 2425 days ago

  #Short #read #alignment: an #introduction https://www.sevenbridges.com/short-read-alignment-algorithms/
• • Jit@jit.aber

  

  Jit bookmarked BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive... 2425 days ago

  BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...

  http://bix.ucsd.edu/projects/blasr/
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and... 2425 days ago

  CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous...

  http://ecogenomics.github.io/CheckM/

  Comments

  • • Neel@neelam

    

    Neel 886 days ago

    CheckM for Metagenome https://linsalrob.github.io/ComputationalGenomicsManual/CheckM/

  • • Neel@neelam

    

    Neel 886 days ago

    MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a bookmark poRe: an R package for the visualization and analysis of nanopore sequencing data 2425 days ago

  We now need to install the poRe dependencies in R, which is very easy: R source("http://www.bioconductor.org/biocLite.R") biocLite("rhdf5") install.packages(c("shiny","bit64","data.table","svDialogs")) q() R may ask if you want...
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a page titled SPAdes hybrid genome assembly 2425 days ago

   use SPAdes to assemble the data.  SPAdes is a swiss-army knife of genome assembly tools, and by default includes read correction.  This takes up lots of RAM, so we are going to skip it.  We will also only use 3 kmers to save...

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