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- Jitendra Prajapati@jprajapati81
Jitendra Prajapati bookmarked QUAST: quality assessment tool for genome assemblies 3722 days ago

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison. More...

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long
Comments
- Jit@jit.aber
  
  Jit 3469 days ago
  You can also try LAZER, it produces the same evaluation as Quast but is 5.6 times faster and use half the memory
  http://www.csd.uwo.ca/~ilie/LASER/
- Jit@jit.aber
  
  Jit 3316 days ago
  Understanding the terms used in QUAST http://quast.bioinf.spbau.ru/manual.html
- Jit@jit.aber
Jit asked GLIBC_2.14 error with SatsumaSynteny !! 3722 days ago

I run SatsumaSynteny on my server using following command: [jit@hm satsuma-code-0]$ ./SatsumaSynteny -q Genome/renamedG.fa -t Genome/genome_v4.fasta -o Genome/OutFile -m 128 -ni 10 -n 256 -chain_only But it kill the program with followng...
- Jit@jit.aber
Jit bookmarked PEAR: a fast and accurate Illumina Paired-End reAd mergeR 3722 days ago

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...

http://www.exelixis-lab.org/web/software/pear
- Jit@jit.aber
Jit posted to the wire 3722 days ago

#R #PiratePlot are cool, and impressive http://www.r-bloggers.com/the-pirate-plot-2-0-the-rdi-plotting-choice-of-r-pirates/
- Priya Singh@priyasingh
Priya Singh posted a new ad in the Opportunity Ph.D. Programme in Computational Biology 3722 days ago
- Priya Singh@priyasingh
Priya Singh bookmarked RACA: Reference-Assisted Chromosome Assembly 3722 days ago

Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end...

http://bioen-compbio.bioen.illinois.edu/RACA/
Comments
- Jit@jit.aber
  
  Jit 3542 days ago
  Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process.
  More at http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0141-6
  Script at https://github.com/gtamazian/chromosomer
- Priya Singh@priyasingh
Priya Singh bookmarked Sequence assembly with MIRA 4 3722 days ago

MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion...

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
Comments
- Neel@neelam
  
  Neel 2305 days ago
  MIRA5 is ready to use http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
- Neel@neelam
Neel bookmarked PAired-eND Assembler for DNA sequences 3722 days ago

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseq

https://github.com/neufeld/pandaseq
- Neel@neelam
Neel posted to the wire 3722 days ago

PAired-eND Assembler for DNA sequences https://github.com/neufeld/pandaseq #Sequence #Assembler #PANDAseq
- Abhi@abhinav
Abhi posted to the wire 3723 days ago

#ConPADE: Genome #Assembly Ploidy Estimation from #Next-Generation Sequencing Data http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004229
- Abhi@abhinav
Abhi posted to the wire 3723 days ago

Hapsembler http://compbio.cs.toronto.edu/hapsembler/hapsembler-2.1_manual.pdf
- Abhi@abhinav
Abhi posted to the wire 3723 days ago

PLATform for Assembling NUcleotide Sequences http://platanus.bio.titech.ac.jp/ #Platanus #Assembler #Genome
- Abhi@abhinav
Abhi posted to the wire 3723 days ago

A universal genomic #coordinate translator for comparative genomics https://github.com/nedaz/kraken #Genes #Translator #Synteny
- Abhi@abhinav
Abhi posted to the wire 3723 days ago

Annotation transfer pipeline MAKER http://gmod.org/wiki/MAKER_Tutorial_2013 #Maker #Annotation #Pipeline
- Thangapandi@Thangapandi
Thangapandi is now a friend with Abhi 3723 days ago
Thangapandi@Thangapandi
Abhi@abhinav
- Abhi@abhinav
Abhi is now a friend with Thangapandi 3723 days ago
Abhi@abhinav
Thangapandi@Thangapandi
- Nishi Singh@nishi
Nishi Singh is now a friend with Priya Singh 3724 days ago
Nishi Singh@nishi
Priya Singh@priyasingh
- Priya Singh@priyasingh
Priya Singh is now a friend with Nishi Singh 3724 days ago
Priya Singh@priyasingh
Nishi Singh@nishi
- Nishi Singh@nishi
Nishi Singh posted a new ad in the Opportunity Research Fellow Bioinformatics 3724 days ago
- Nishi Singh@nishi
Nishi Singh posted a new ad in the Opportunity One-Year Internship In Computational Biology & Bioinformatics 3724 days ago

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