BOL: All Site Activity

All Site Activity

- Jit@jit.aber
Jit posted to the wire 2620 days ago

hybrid assembly pipeline for bacterial genomes with Unicycler: https://github.com/rrwick/Unicycler #Unicycler #Hybrid #Bacteria
- Jit@jit.aber
Jit posted to the wire 2621 days ago

Sort a file with column 2: sort -g -k 2,2 allPacbio.fa.fai > sorted.fai #sort #file #column
- Jit@jit.aber
Jit posted to the wire 2622 days ago

Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq
- Jit@jit.aber
Jit bookmarked QuorUM: An Error Corrector for Illumina Reads 2622 days ago

Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh created a new bio-script Convert newline formated sequence into fasta format with perl 2622 days ago
- Jit@jit.aber
Jit answered the question How to remove a fasta sequence by header from a multifasta file ? 2622 days ago

Try BBMAP filterbyname.sh in=file.fa out=filtered.fa names=contig1,contig2
- Archana Malhotra@archana
Archana Malhotra asked How to remove a fasta sequence by header from a multifasta file ? 2622 days ago

>AAAAGTCGTGC >BBBAGTGCGGGTG Remove AAA and keep only BBB
- Jit@jit.aber
Jit posted to the wire 2623 days ago

De Bruijn graph Tutorial http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf #Assembly #Tutorial #DeBruijn
- Jit@jit.aber
Jit answered the question What are the best approach that gave good results in genome projects? 2623 days ago

One interesting approach that gave good results in other genome projects - do several cycles of SSPACE / GapCloser/ REAPR (to detect misassemblies and break them). Usually after 4-6 cycles this converge on an optimal assembly and the statistics...
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh created a page Alignment-free sequence comparison tools available for next-generation sequencing data analysis 2623 days ago

kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...
Comments
- Rahul Nayak@rahul
  
  Rahul Nayak 2504 days ago
  AlFree tool for alingment of sequence at http://150.254.122.234:8000/
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh asked What are the best approach that gave good results in genome projects? 2623 days ago

I am working on genome assembly, but wordering the optimised method to achieve the best result. Your comments and suggestions are welcome.
- Jit@jit.aber
Jit bookmarked Meraculous: De Novo Genome Assembly with Short Paired-End Reads 2623 days ago

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/
- Jit@jit.aber
Jit posted to the wire 2623 days ago

Understanding alignment https://www.cs.umd.edu/class/fall2011/cmsc858s/Alignment.pdf #Alignment #Learn
- Strand@Strand
Strand published a news post Webinar on Unique Molecular Identifier (UMI)-powered Ultra-sensitive Variant Calling using Strand... 2623 days ago
Comments
- Strand@Strand
  
  Strand 2587 days ago
  Hurry! Limited seats available. To attend, register at http://www.strand-ngs.com/webinar_registration
- Archana Malhotra@archana
Archana Malhotra created a new bio-script Genetic Algorithms demonstration with word DNA in Perl 2624 days ago
- Jit@jit.aber
Jit posted to the wire 2624 days ago

Genetic algorithms with Python https://github.com/handcraftsman/GeneticAlgorithmsWithPython #Python #GA
- Jit@jit.aber
Jit posted to the wire 2624 days ago

We are still working on to fix some of the missing BOL data. sorry for the inconvenience caused. #BOL #Work #Data #Missing #Recover
- Yeshodari@Yeshodari
Yeshodari published a news post Strand Life Sciences announces the release of Strand NGS v3.1 at ASHG 2017 2638 days ago

Strand Life Sciences announces the release of Strand NGS v3.1 at ASHG 2017
- Yeshodari@Yeshodari
Yeshodari bookmarked Strand Life Sciences announces the release of Strand NGS v3.1 at ASHG 2017 2638 days ago

Strand Life Sciences announces the release of Strand NGS v3.1 at ASHG 2017 ORLANDO, USA, Oct 17, 2017/ PRNewswire/ Strand NGS now supports large scale RNA- and small-RNA-Seq and Unique Molecular Identifiers (UMIs) for DNA-, RNA-, and...

http://www.strand-ngs.com/strand-announce-strandngss-v31
- Rahul Agarwal@raag
Rahul Agarwal commented on the file Bioinformatics approach to Boar Taint 2646 days ago

Fine mapping of a QTL affecting levels of skatole on pig chromosome 7 https://bmcgenet.biomedcentral.com/articles/10.1186/s12863-017-0549-8

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