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- Jit@jit.aber
Jit bookmarked PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool 2599 days ago

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...

https://plast.inria.fr/
- Jit@jit.aber
Jit bookmarked collinearity: scripts to parse and analyse MCScanX collinearity output 2600 days ago

scripts to parse and analyse MCScanX collinearity output

https://github.com/reubwn/collinearity
Comments
- Jit@jit.aber
  
  Jit 1762 days ago
  This python script is by far the best for MCscan
  https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
- Jit@jit.aber
Jit bookmarked Scripts for the analysis of HGT in genome sequence data. 2600 days ago

Scripts for the analysis of HGT in genome sequence data

https://github.com/reubwn/hgt
- Jit@jit.aber
Jit bookmarked phyloXML: XML for evolutionary biology and comparative genomics 2601 days ago

phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch...

http://www.phyloxml.org/
- Jit@jit.aber
Jit bookmarked Ribbon: Visualizing complex genome alignments and structural variation: 2601 days ago

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...

http://genomeribbon.com/
- Jit@jit.aber
Jit bookmarked Bioinformatics lectures ! 2601 days ago

Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to...

https://rob-p.github.io/CSE549F16/lectures/
- Jit@jit.aber
Jit bookmarked Computational Genomics: Applied Comparative Genomics 2601 days ago

The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing...

https://github.com/schatzlab/appliedgenomics
- Jit@jit.aber
Jit bookmarked Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome 2601 days ago

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...

http://schatzlab.cshl.edu/data/nanocorr/
- Jit@jit.aber
Jit posted to the wire 2601 days ago

Linux command to find the file contains a string "LOCK_EX": grep -Ril "LOCK_EX" / #Root #Find #Linux #Grep #search
- Jit@jit.aber
Jit bookmarked simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data 2602 days ago

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from...

https://www.ebi.ac.uk/goldman-srv/simNGS/
- Robert M Willioms@robert
Robert M Willioms created a page RNAseq data analysis links ! 2602 days ago

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment,...
- Robert M Willioms@robert
Robert M Willioms created a page Single Cell RNAseq data analysis tutorial !! 2602 days ago

A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the average expression level for each gene across a large population of input cells Useful for comparative transcriptomics,...
- Robert M Willioms@robert
Robert M Willioms bookmarked DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing 2602 days ago

"DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitating the procedure...

https://compcytogen.pensoft.net/articles.php?id=20830
- Robert M Willioms@robert
Robert M Willioms answered the question How to resolve this NanoPlot error NanoImportError: No module named concurrent.futures 2602 days ago

You should try installing pip install futures Futures feature has never included in Python 2.x core. However, it's present in Python 3.x since Python 3.2.
- Jit@jit.aber
Jit bookmarked INC-Seq: accurate single molecule reads using nanopore sequencing 2603 days ago

INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...

https://github.com/CSB5/INC-Seq
- Jit@jit.aber
Jit bookmarked Opera: An optimal genome scaffolding program 2603 days ago

Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...

https://sourceforge.net/projects/operasf/
- Jit@jit.aber
Jit bookmarked RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data 2603 days ago

RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to...

http://kiwi.cs.dal.ca/Software/RITA
- Jit@jit.aber
Jit created a page SPAdes hybrid genome assembly 2603 days ago

When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the...
Comments
- Rahul Nayak@rahul
  
  Rahul Nayak 2426 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 time:
  ./SPAdes-3.6.2-Linux/bin/spades.py --only-assembler -t 4 -k 21,51,71 -1 SRR2627175_1.fastq.gz -2 SRR2627175_2.fastq.gz --nanopore minion.pass.2D.fastq -o SPAdes_hybrid &
  Use samtools to extract the top contig:
  head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid/contigs.fasta NODE_1_length_4620446_cov_135.169_ID_22238 > single_contig.fa
  Finally, a quick comparison to the reference:
  sudo apt-get install mummer curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000913.3&rettype=fasta&retmode=txt" > NC_000913.3.fa nucmer NC_000913.3.fa single_contig.fa mummerplot -png out.delta display out.png &
- Jit@jit.aber
Jit bookmarked miniasm: very fast OLC-based de novo assembler for noisy long reads 2603 days ago

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...

https://github.com/lh3/miniasm
- Jit@jit.aber
Jit bookmarked coursera genome assembly tutorial 2605 days ago

Solutions to Coursera Genome Sequencing (Bioinformatics II)

https://github.com/iansealy/coursera-assembly

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