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• • Neel@neelam

  

  Neel bookmarked RestrictionDigest: A powerful Perl module for simulating genomic restriction digests 3014 days ago

  RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes...

  https://github.com/JINPENG-WANG/RestrictionDigest
• • Neel@neelam

  

  Neel posted to the wire 3014 days ago

  sed -i -e '/^+/,/^\@/{/^+/!{/^\@/!d}}; /^+/ d; s/@/>/g' OUTPUT.fastq > out.fa #Convert
• • Neel@neelam

  

  Neel answered the question What are the best software options available for nanopore (ONT) reads ? 3014 days ago

  Please visit this https://bioinformaticsonline.com/search?q=ont&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities
• • Jit@jit.aber

  

  Jit bookmarked Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from... 3014 days ago

  Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by...

  https://github.com/ruping/Breakpointer
• • Jit@jit.aber

  

  Jit bookmarked P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads 3014 days ago

  P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...

  http://www.fishbrowser.org/software/P_RNA_scaffolder/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh created a new bio-script Perl script to check fastq reads qualities ! 3015 days ago
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh created a new bio-script Perl script to find palindromic regions in DNA sequences 3015 days ago
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh voted on the poll Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects? 3015 days ago
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh voted on the poll What programming language do you hate the most? 3015 days ago
• • Jit@jit.aber

  

  Jit bookmarked HiGlass: a tool for exploring genomic contact matrices and tracks. 3015 days ago

  HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass...

  http://higlass.io/
• • Jit@jit.aber

  

  Jit bookmarked D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way 3015 days ago

  D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...

  http://dgenies.toulouse.inra.fr/
• • Shruti Paniwala@shruti

  

  Shruti Paniwala created a new bio-script Perl script to find coding regions in DNA sequences 3015 days ago
• • Shruti Paniwala@shruti

  

  Shruti Paniwala posted to the wire 3015 days ago

  Finding coding regions in DNA sequences http://genome.crg.es/courses/Lisbon04/exercises/day2/Perl_programming/index.html #Perl #Genes #Script
• • Shruti Paniwala@shruti

  

  Shruti Paniwala bookmarked GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or... 3015 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 3015 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 3016 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++. 3016 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 3018 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 2952 days ago

     

    1. 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).

    2. Using AlignGraph

       runHALC.py long_reads.fa contigs.fa [-options|-options]
• • Jit@jit.aber

  

  Jit posted to the wire 3018 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 3018 days ago

  Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

  http://lindenb.github.io/jvarkit/

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