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- Jit@jit.aber
Rahul Nayak chose the best answer to the question What are the best software options available for nanopore (ONT) reads ? 2425 days ago

I recommend to have a look at this BOL For De-novo Genome Assembly -- Canu. Flye and MARVEL sound promising.Alignment -- minimap2 and/or LAST, depending on the application. LAST is particularly good...
- Rahul Nayak@rahul
Rahul Nayak bookmarked bpRNA: large-scale automated annotation and analysis of RNA secondary structure 2425 days ago

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...

http://github.com/hendrixlab/bpRNA
- Poonam Mahapatra@poonam
Poonam Mahapatra commented on a bookmark CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. 2426 days ago

Canu is one of the best de novo assemblers available for long reads - it’s a fork and updated version of the Celera assembler that was used to assemble the human genome. It is quite a complex beast that has HPC integration built in -...
- Poonam Mahapatra@poonam
Poonam Mahapatra commented on a page titled Run miniasm assembler on nanopore reads ! 2426 days ago

I followed this to assemble the genome using ONT (nanopore reads) Minimap and miniasm are ultrafast tools for (i) mapping and (ii) assembly. Designed for long, noisy reads, they do not have a correction or consensus step, and therefore the...
- Jit@jit.aber
Jit bookmarked Hapsembler: An Assembler for Highly Polymorphic Genomes 2426 days ago

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454....

http://compbio.cs.toronto.edu/hapsembler/
- Jit@jit.aber
Jit bookmarked DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications 2427 days ago

we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a...

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822/
- Jit@jit.aber
Jit posted to the wire 2430 days ago

#N50 = contig length so that half of the contigs are longer and 1/2 of contigs are shorter
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary created a page Ancestral sequence reconstruction steps ! 2430 days ago

Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an...
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- Jit@jit.aber
  
  Jit 2372 days ago
  Parallelization of MAFFT for large-scale multiple sequence alignmentshttps://academic.oup.com/bioinformatics/article/34/14/2490/4916099
- Anjana@anjana
Anjana is now a friend with Nirmal Pal 2431 days ago
Anjana@anjana
Nirmal Pal@nibex
- Nirmal Pal@nibex
Nirmal Pal is now a friend with Anjana 2431 days ago
Nirmal Pal@nibex
Anjana@anjana
- Nitesh@prince26121991
Nitesh posted a new ad in the Opportunity Bioinformatics Project Assistant Level II position at CSIR - Institute of Himalayan Bioresource... 2431 days ago
- Rahul Nayak@rahul
Rahul Nayak created a new bio-script Biological Sequence handling with Perl ! 2432 days ago
- Jit@jit.aber
Jit replied on the discussion topic Python vs Perl in the group Python Everywhere 2432 days ago

This made me think of Perl https://benchmarksgame-team.pages.debian.net/benchmarksgame/faster/perl.html . #PerlLove
- Aasha@aasha
Aasha posted a new ad in the Opportunity Bioinformatics jobs at NIBMG 2432 days ago
- Poonam Mahapatra@poonam
Poonam Mahapatra bookmarked TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest... 2433 days ago

TACOA is a software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. TACOA can be easily installed and run on a...

http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa
- Poonam Mahapatra@poonam
Poonam Mahapatra posted to the wire 2433 days ago

Convert 2bit to psl $ blat myAssembly.2bit -oneOff=0 -noHead myQueryContigSeqs.fa myHits.psl #Convert #psl #2bit #blat
- Poonam Mahapatra@poonam
Poonam Mahapatra posted to the wire 2433 days ago

Convert fasta to 2bit $ faToTwoBit myAssembly.fa myAssembly.2bit #Fasta #2bit #Convert
- Poonam Mahapatra@poonam
Poonam Mahapatra bookmarked Circlator: automated circularization of genome assemblies using long sequencing reads 2433 days ago

A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...

http://sanger-pathogens.github.io/circlator/
- Jit@jit.aber
Jit bookmarked TULIP - The Uncorrected Long read Integration Pipeline 2433 days ago

TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long...

https://github.com/Generade-nl/TULIP
- Jit@jit.aber
Jit created a page Frequent Paired-end reads (PE 2x100) mapping command lines 2433 days ago

bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...

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