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• • Jit@jit.aber

  

  Jit posted to the wire 3018 days ago

  PacBio genome assembly tools https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx147/4590140 #PacBio #Assembly #Tools #SMRT #LongReads
• • Rahul Nayak@rahul

  

  Rahul Nayak published a blog post Understanding liftOver ! 3020 days ago

  LiftOver is a necesary step to bring all genetical analysis to the same reference build.
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked Cerulean: A hybrid assembly using high throughput short and long reads 3021 days ago

  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...

  https://sourceforge.net/projects/ceruleanassembler/
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead... 3021 days ago

  PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...

  https://github.com/hitbio/PERGA
• • Jit@jit.aber

  

  Jit bookmarked EAGLER: a scaffolding tool for long reads. 3022 days ago

  EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...

  https://github.com/mculinovic/EAGLER
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra bookmarked “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files 3023 days ago

  One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...

  http://doua.prabi.fr/software/one-code-to-find-them-all
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra bookmarked MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times 3024 days ago

  MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy...

  http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra bookmarked GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence 3024 days ago

  GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...

  https://sourceforge.net/projects/glean-gene/
• • Poonam Mahapatra@poonam

  

  Poonam Mahapatra bookmarked Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment 3024 days ago

  Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...

  http://molevol.cmima.csic.es/castresana/Gblocks_server.html
• • Rahul Nayak@rahul

  

  Rahul Nayak created a page Gap filling or Contigs extensions tools ! 3025 days ago

  There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward almost closed genomes with GapFiller". There are also some tools like...
• • Jit@jit.aber

  

  Jit bookmarked Ranbow: a haplotype assembler for polyploid genomes 3025 days ago

  Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...

  https://www.molgen.mpg.de/ranbow
• • Jit@jit.aber

  

  Jit bookmarked BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing... 3026 days ago

  BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...

  https://github.com/lh3/bfc
• • Jit@jit.aber

  

  Jit bookmarked CrossMap: a program for convenient conversion of genome coordinates 3026 days ago

  CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly...

  http://crossmap.sourceforge.net
• • Surabhi Chaudhary@surabhi

  

  Surabhi Chaudhary bookmarked SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms 3027 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 3027 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 ! 3027 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 ! 3028 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 3028 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 3028 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 3028 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

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