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- Jit@jit.aber
Jit published a blog post List of perl special symbols ! in the group Perl *PIPERs 1761 days ago

Perl is know for symbols !
- Jit@jit.aber
Jit answered the question Can anyone suggest me a bioinformatics pipeline management tools ? 1761 days ago

There's lots of tools for pipelines in Python. They are sophisticated that helps you decompose an analysis into parts and runs it robustly. Snakemake is my favourite. It's (nearly) pure Python and can generate reports. Nextflow is...
- Neel@neelam
Neel asked Can anyone suggest me a bioinformatics pipeline management tools ? 1761 days ago

Hi, I am looking for a bioinformatics pipeline management tools to manage my new bioinfo pipeline. Can anyone at BOL suggest me an easy to use tool.
- Jit@jit.aber
Jit posted to the wire 1761 days ago

Python daemon thread https://www.journaldev.com/16152/python-daemon-thread #Python #Thread
- Jit@jit.aber
Jit commented on the bio-script Perl6 script to count ATGC ! 1761 days ago

Yes, indeed intersting but complex script script in Perl v6 More at https://examples.p6c.dev/categories/rosalind.html
- Poonam Mahapatra@poonam
Poonam Mahapatra created a new bio-script Perl6 script to count ATGC ! 1761 days ago
Comments
- Jit@jit.aber
  
  Jit 1761 days ago
  Yes, indeed intersting but complex script script in Perl v6
  More at https://examples.p6c.dev/categories/rosalind.html
- Jit@jit.aber
Jit bookmarked The Raku Programming Language 1761 days ago

Raku is a member of the Perl family of programming languages. Formerly known as Perl 6, it was renamed in October 2019. Raku introduces elements of many modern and historical languages. Compatibility with Perl was not a goal, though a compatibility...

https://www.raku.org/
Comments
- Jit@jit.aber
  
  Jit 1748 days ago
  Learn Raku by example https://uzluisf.gitlab.io/raku-by-example/
- Rahul Nayak@rahul
  
  Rahul Nayak 1739 days ago
  Nice discussion here about Raku and Python https://news.ycombinator.com/item?id=21227571
- Rahul Nayak@rahul
  
  Rahul Nayak 1737 days ago
  Try online interface to run your Raku programs
  https://glot.io/new/perl6
  A nice place to test and check the program on cloud
+6 more
- Jit@jit.aber
Jit commented on a bookmark EFS: an ensemble feature selection tool implemented as R-package and web-application 1761 days ago

A review of ensembles for feature selection is described. Current state-of-the-art is provided. Types of ensembles, combination methods and evaluation measures are described. Some challenges and future trends are provided. all...
- Jit@jit.aber
Jit bookmarked EFS: an ensemble feature selection tool implemented as R-package and web-application 1761 days ago

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in...

http://efs.heiderlab.de/
Comments
- Jit@jit.aber
  
  Jit 1761 days ago
  A review of ensembles for feature selection is described.
  Current state-of-the-art is provided.
  Types of ensembles, combination methods and evaluation measures are described.
  Some challenges and future trends are provided.
  all at https://www.sciencedirect.com/science/article/pii/S1566253518303440
- Neel@neelam
Neel created a new bio-script Bash script to alignment of short reads against reference genome ! 1761 days ago
- Jit@jit.aber
Jit created a new bio-script Bash script to download SRA file ! 1761 days ago
- Jit@jit.aber
Jit bookmarked mutatrix: a population genome simulator which generates simulated genomes. 1761 days ago

genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphisms More at https://github.com/ekg/mutatrix ./mutatrix -S sample -P test/ -p 2 -n 10 reference.fasta

https://github.com/ekg/mutatrix
- Jit@jit.aber
Jit bookmarked Glia: a Graph/Smith-Waterman (partial order) aligner/realigner 1761 days ago

glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f...

https://github.com/ekg/glia
- Jit@jit.aber
Jit bookmarked VG: variation graph data structures, interchange formats, alignment, genotyping, and variant... 1761 days ago

Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...

https://github.com/vgteam/vg
- Jit@jit.aber
Jit posted to the wire 1761 days ago

NGS alignment and variant calling tutorial https://github.com/ekg/alignment-and-variant-calling-tutorial #NGS #variant #snp #tools #tutorial #calling
- Jit@jit.aber
Jit bookmarked vt: a variant tool set that discovers short variants from Next Generation Sequencing data. 1761 days ago

vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt

https://genome.sph.umich.edu/wiki/Vt
- Jit@jit.aber
Jit bookmarked MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants 1761 days ago

MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being...

https://github.com/AlgoLab/malva
- Jit@jit.aber
Jit bookmarked Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search 1761 days ago

Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...

https://github.com/redayounsi/2KP2P
- Jit@jit.aber
Jit bookmarked FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads 1761 days ago

FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...

http://bioinfo.ut.ee/FastGT/
- Jit@jit.aber
Jit bookmarked Kevler: Reference-free variant discovery in large eukaryotic genomes 1761 days ago

Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...

https://github.com/kevlar-dev/kevlar

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