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• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked SPAdes 3193 days ago

  SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...

  http://bioinf.spbau.ru/spades

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  • • Jit@jit.aber

    

    Jit 2599 days ago

    Common usage 

    SPAdes: de Bruijn graph based assembler

    The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is automatically selected by SPAdes using the maximum read length of the input data, and each individual kmer contributes to the final assembly. To run SPAdes we will use the spades.py command with the --careful option to minimize the number of mismatches in the contigs, -o for the output folder, -1 for the path to the forward reads, -2 for the path to the reverse reads, and -s for the path to the singles reads. If desired, a list of kmers can be specified with the -k flag which will override automatic kmer selection.

    spades.py --careful -o SPAdes_out -1 /common/Assembly_Tutorial/Quality_Control/Sample_1.fastq -2 /common/Assembly_Tutorial/Quality_Control/Sample_2.fastq -s /common/Assembly_Tutorial/Quality_Control/Sample_s.fastq

     
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked DISCOVAR 3194 days ago

  DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...

  https://www.broadinstitute.org/software/discovar/blog/
• • Abhi@abhinav

  

  Abhi bookmarked LASTZ 3194 days ago

  LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as...

  http://www.bx.psu.edu/~rsharris/lastz/

  Comments

  • • Shruti Paniwala@shruti

    

    Shruti Paniwala 3107 days ago

    The latest relase of LastZ at http://www.bx.psu.edu/~rsharris/lastz/newer/

  • • Jit@jit.aber

    

    Jit 2542 days ago

    Understanding lastz http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf
• • Jit@jit.aber

  

  Jit bookmarked Trimmomatic: A flexible read trimming tool for Illumina NGS data 3197 days ago

  Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10...

  http://www.usadellab.org/cms/?page=trimmomatic
• • Jit@jit.aber

  

  Jit bookmarked Understanding Fastqc Output 3197 days ago

  Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...

  http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/
• • Jit@jit.aber

  

  Jit answered the question GLIBC_2.14 error with SatsumaSynteny !! 3197 days ago

  You should recompile this code using:make clean && nice -n19 make
• • Surabhi Chaudhary@surabhi

  

  Surabhi Chaudhary bookmarked SCALCE 3197 days ago

  SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any...

  http://sfu-compbio.github.io/scalce/
• • parul@parul

  

  parul published a news post Predictions from Fred Bazzoli, Editor of Health Data Management 3198 days ago
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  parul is now a friend with Shruti Paniwala 3198 days ago

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• • Shruti Paniwala@shruti

  

  Shruti Paniwala is now a friend with parul 3198 days ago

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  parul is now a friend with karimse07 3198 days ago

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  karimse07 is now a friend with parul 3198 days ago

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  parul is now a friend with Nishi Singh 3198 days ago

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• • Nishi Singh@nishi

  

  Nishi Singh is now a friend with parul 3198 days ago

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• • parul@parul

  

  parul joined the group Metabolomics 3198 days ago
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  parul joined the group Web prgramming for biologist/bioinformatician 3198 days ago
• • Jitendra Prajapati@jprajapati81

  

  Jitendra Prajapati posted to the wire 3198 days ago

  Genes and Genome https://genestogenomes.org/tag/chromosomes/
• • Jit@jit.aber

  

  Jit posted a new ad in the Opportunity JRF Bioinformatics at NIPGR 3198 days ago
• • Amala Arumugam@Amala

  

  Amala Arumugam is now a friend with Jitendra Prajapati 3201 days ago

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