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- Abhimanyu Singh@abhimanyu
Abhimanyu Singh voted on the poll Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects? 2361 days ago
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh voted on the poll What programming language do you hate the most? 2361 days ago
- Jit@jit.aber
Jit bookmarked HiGlass: a tool for exploring genomic contact matrices and tracks. 2362 days ago

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass...

http://higlass.io/
- Jit@jit.aber
Jit bookmarked D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way 2362 days ago

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...

http://dgenies.toulouse.inra.fr/
- Shruti Paniwala@shruti
Shruti Paniwala created a new bio-script Perl script to find coding regions in DNA sequences 2362 days ago
- Shruti Paniwala@shruti
Shruti Paniwala posted to the wire 2362 days ago

Finding coding regions in DNA sequences http://genome.crg.es/courses/Lisbon04/exercises/day2/Perl_programming/index.html #Perl #Genes #Script
- Shruti Paniwala@shruti
Shruti Paniwala bookmarked GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or... 2362 days ago

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...

https://academic.oup.com/bioinformatics/article/31/23/3733/209212
- Shruti Paniwala@shruti
Shruti Paniwala bookmarked npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads 2362 days ago

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...

http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html
- Shruti Paniwala@shruti
Shruti Paniwala bookmarked BEAP: Blast Extension and Assembly Program 2362 days ago

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that...

https://www.animalgenome.org/tools/beap/
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary bookmarked PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. 2362 days ago

We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...

http://derisilab.ucsf.edu/software/price/
- Jit@jit.aber
Jit bookmarked HALC: High throughput algorithm for long read error correction 2365 days ago

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...

https://github.com/lanl001/halc
Comments
- Jit@jit.aber
  
  Jit 2299 days ago
  
  Inputs
  
  Long reads in FASTA format.
  
  Contigs assembled from the corresponding short reads in FASTA format.
  
  The initial short reads in FASTA format (only for -ordinary mode; obtained with cat left_reads.fa >short_reads.fa and then cat right_reads.fa >>short_reads.fa).
  
  Using AlignGraph
  
  runHALC.py long_reads.fa contigs.fa [-options|-options]
- Jit@jit.aber
Jit posted to the wire 2365 days ago

reformat.sh in=reads.fq out=highQuality.fq maq=16 (that will throw away all reads with average quality below 16) #Filter #BBMap #Quality
- Jit@jit.aber
Jit bookmarked Jvarkit : Java utilities for Bioinformatics 2365 days ago

Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

http://lindenb.github.io/jvarkit/
- Jit@jit.aber
Jit posted to the wire 2365 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 ! 2367 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 2368 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... 2368 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. 2369 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 2369 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 2371 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

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