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- Jit@jit.aber
Jit bookmarked Bokeh: An interactive visualization library that targets modern web browsers for presentation 2298 days ago

Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very...

https://bokeh.pydata.org/en/latest/
- Jit@jit.aber
Jit bookmarked NanoPack: visualizing and processing long-read sequencing data 2298 days ago

The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...

https://github.com/wdecoster/nanoQC
- Neel@neelam
Neel bookmarked FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform 2298 days ago

FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use...

https://github.com/holtjma/fmlrc
- Jit@jit.aber
Jit bookmarked mmgenome: Tools for extracting individual genomes from metagneomes 2299 days ago

The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole...

https://github.com/MadsAlbertsen/mmgenome
- Jit@jit.aber
Jit posted to the wire 2299 days ago

perl -pe '/^>/ ? print "\n" : chomp' LR.fasta | tail -n +2 > out.fasta #singleLine #Multifasta #Multi2Single
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh created a new bio-script Perl script to extract sequence by Ids from multifasta file ! 2299 days ago
- Jit@jit.aber
Jit created a page List of non-commercial NGS genotype-calling software 2299 days ago

Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and...
Comments
- Rahul Nayak@rahul
  
  Rahul Nayak 1346 days ago
  Delly – Structural variant discovery by integrated paired-end and split-read analysis. [ paper-2012 ]
  lumpy – lumpy: a general probabilistic framework for structural variant discovery. [ paper-2014 ]
  manta – Structural variant and indel caller for mapped sequencing data. [ paper-2015 ]gridss – GRIDSS: the Genomic Rearrangement IDentification Software Suite. [ paper-2017 ]smoove – structural variant calling and genotyping with existing tools, but,smoothly.
- Jit@jit.aber
Jit bookmarked PureCN: copy number calling and SNV classification using targeted short read sequencing 2299 days ago

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...

http://bioconductor.org/packages/release/bioc/html/PureCN.html
- Rahul Nayak@rahul
Rahul Nayak bookmarked VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting,... 2301 days ago

VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF...

http://vcftools.sourceforge.net/perl_module.html
- Jit@jit.aber
Jit created a new bio-script Install Python locally on shared Linux server ! 2301 days ago
- Jit@jit.aber
Jit bookmarked AlignQC: A tool for assessing an alignment, and generating reports that are easy to share 2301 days ago

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...

https://www.healthcare.uiowa.edu/labs/au/AlignQC/
- Jit@jit.aber
Jit created a new bio-script Installing NextSV on Ubuntu ! 2302 days ago
- Jit@jit.aber
Jit bookmarked NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data 2302 days ago

NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...

https://github.com/Nextomics/NextSV
- Jit@jit.aber
Jit bookmarked gSearch: a fast and flexible general search tool for whole-genome sequencing 2302 days ago

gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...

http://ml.ssu.ac.kr/gSearch/index.html
- Rahul Nayak@rahul
Rahul Nayak bookmarked Fastq stats in Emoji :) 2302 days ago

Read one or more FASTQ files, fastqe will compute quality stats for each file and print those stats as emoji... for some reason. Given a fastq file in Illumina 1.8+/Sanger format, calculate the mean (rounded) score for each position and...

https://github.com/lonsbio/fastqe
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 2302 days ago

Understanding PairedEnd(PE) mapping https://davetang.org/muse/2014/07/24/getting-started-paired-end-reads/ #PE #Paired #End #PairedEnd #Mapping #Map #Learn
- Rahul Nayak@rahul
Rahul Nayak commented on a bookmark CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. 2302 days ago

➜ bin git:(master) ✗ ./canu usage: canu [-version] [-citation] \ [-correct | -trim | -assemble | -trim-assemble] \ [-s <assembly-specifications-file>] \ -p <assembly-prefix> \ -d <assembly-directory> \...
- Rahul Nayak@rahul
Rahul Nayak created a new bio-script Perl script to find palindromic pattern ! 2302 days ago
- Jit@jit.aber
Jit created a new bio-script Running REAPR ! 2302 days ago
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 2302 days ago

du -sh * | sort | grep "G" #List size of all the directory #Size #List #Directory #Linux

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