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- Shruti Paniwala@shruti
Shruti Paniwala bookmarked GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or... 2406 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 2406 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 2406 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++. 2406 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 2409 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 2343 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 2409 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 2409 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 2409 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 ! 2411 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 2412 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... 2412 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. 2413 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 2413 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 2415 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 2415 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 2415 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 ! 2416 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 2416 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... 2417 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 2417 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

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