<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40598?offset=140 https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly Wed, 06 Dec 2017 02:08:14 -0600 https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly <![CDATA[COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly]]> An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads Mon, 30 Apr 2018 04:38:40 -0500 https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads <![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]> ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. 

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

]]> Seema Singh https://bioinformaticsonline.com/bookmarks/view/41673/lr-gapcloser-a-tiling-path-based-gap-closer-that-uses-long-reads-to-complete-genome-assembly Thu, 14 May 2020 15:09:52 -0500 https://bioinformaticsonline.com/bookmarks/view/41673/lr-gapcloser-a-tiling-path-based-gap-closer-that-uses-long-reads-to-complete-genome-assembly <![CDATA[LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly]]> LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38735/genome-assembly-tutorial-genome-assembly-for-short-and-long-reads Sat, 19 Jan 2019 17:29:53 -0600 https://bioinformaticsonline.com/bookmarks/view/38735/genome-assembly-tutorial-genome-assembly-for-short-and-long-reads <![CDATA[Genome assembly tutorial "Genome Assembly for short and long reads"]]> In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

  1. How to perform basic quality checks on the input data
  2. How to run a short read assembler on Illumina data
  3. How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
  4. How to improve the accuracy of a long read assembly using short reads
  5. How to assess the quality of an assembly

https://bioinformaticsdotca.github.io/high-throughput_biology_2017

Address of the bookmark: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38801/genome-assembly-forensics-finding-the-elusive-mis-assembly Sat, 26 Jan 2019 18:02:01 -0600 https://bioinformaticsonline.com/bookmarks/view/38801/genome-assembly-forensics-finding-the-elusive-mis-assembly <![CDATA[Genome assembly forensics: finding the elusive mis-assembly]]> We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called amosvalidate. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at http://amos.sourceforge.net.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/ 

http://amos.sourceforge.net/wiki/index.php/AMOS

Address of the bookmark: http://amos.sourceforge.net/wiki/index.php/AMOS

]]> Jit https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly Sun, 30 Aug 2020 09:51:38 -0500 https://bioinformaticsonline.com/blog/view/42166/software-for-genome-assembly <![CDATA[Software for genome assembly !]]> List of bioinformatics tools/Software Website References for genome assembly:

1 Falcon https://github.com/PacificBiosciences/pb-assembly

2 Canu assembler http://canu.readthedocs.io/en/latest/index.html

3 Miniasm assembler https://github.com/lh3/miniasm

4 PBJelly scaffolding tool https://sourceforge.net/projects/pb-jelly/

5 ARCS scaffolding tool https://github.com/bcgsc/arcs

6 Redundans reduction and scaffolding tool https://github.com/Gabaldonlab/redundans

7 Arrow error correction https://github.com/PacificBiosciences/ GenomicConsensus

8 PILON error correction https://github.com/broadinstitute/pilon/wiki

9 BUSCO single copy gene markers http://busco.ezlab.org/

10 Bandage graph assembly viewer https://rrwick.github.io/Bandage/

11 Gepard dotter http://cube.univie.ac.at/gepard

12 MUMmer aligner and plotter http://mummer.sourceforge.net/

]]> LEGE https://bioinformaticsonline.com/blog/view/43634/illumina-based-assembly-pipeline-steps Fri, 10 Dec 2021 06:22:54 -0600 https://bioinformaticsonline.com/blog/view/43634/illumina-based-assembly-pipeline-steps <![CDATA[Illumina based assembly pipeline steps !]]> Illumina
  1. Merge re-sequenced FastQ files (cat)
  2. Read QC (FastQC)
  3. Adapter trimming (fastp)
  4. Removal of host reads (Kraken 2; optional)
  5. Variant calling
    1. Read alignment (Bowtie 2)
    2. Sort and index alignments (SAMtools)
    3. Primer sequence removal (iVar; amplicon data only)
    4. Duplicate read marking (picard; optional)
    5. Alignment-level QC (picard, SAMtools)
    6. Genome-wide and amplicon coverage QC plots (mosdepth)
    7. Choice of multiple variant calling and consensus sequence generation routes (iVar variants and consensus; default for amplicon data || BCFTools, BEDTools; default for metagenomics data)
      • Variant annotation (SnpEff, SnpSift)
      • Consensus assessment report (QUAST)
      • Lineage analysis (Pangolin)
      • Clade assignment, mutation calling and sequence quality checks (Nextclade)
      • Individual variant screenshots with annotation tracks (ASCIIGenome)
    8. Intersect variants across callers (BCFTools)
  6. De novo assembly
    1. Primer trimming (Cutadapt; amplicon data only)
    2. Choice of multiple assembly tools (SPAdes || Unicycler || minia)
  7. Present QC and visualisation for raw read, alignment, assembly and variant calling results (MultiQC)
]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/26332/pilon Mon, 08 Feb 2016 15:56:18 -0600 https://bioinformaticsonline.com/bookmarks/view/26332/pilon <![CDATA[Pilon]]> Pilon is a software tool which can be used to:

  • Automatically improve draft assemblies
  • Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

  • Single base differences
  • Small indels
  • Larger indel or block substitution events
  • Gap filling
  • Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/26906/paired-end-assembler-for-dna-sequences Wed, 06 Apr 2016 05:25:34 -0500 https://bioinformaticsonline.com/bookmarks/view/26906/paired-end-assembler-for-dna-sequences <![CDATA[PAired-eND Assembler for DNA sequences]]> PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

 

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

]]> Neel https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs Tue, 10 May 2016 07:46:24 -0500 https://bioinformaticsonline.com/bookmarks/view/27257/busco-assessing-genome-assembly-and-annotation-completeness-with-benchmarking-universal-single-copy-orthologs <![CDATA[BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs]]>
  • High-throughput genomics has revolutionized biological research, however, while the number of sequenced genomes grows by the day, quality assessment of the resulting assembled sequences remains complicated and mostly limited to technical measures like N50. 
  • BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. 
  • BUSCO assessments are implemented in open-source software, with comprehensive lineage-specific sets of Benchmarking Universal Single-Copy Orthologs for arthropods, vertebrates, metazoans, fungi, eukaryotes, and bacteria. 
  • These conserved orthologs are ideal candidates for large-scale phylogenomics studies, and the annotated BUSCO gene models built during genome assessments provide a comprehensive gene predictor training set for use as part of genome annotation pipelines. 
  • BUSCO assessments offer intuitive metrics, based on evolutionarily informed expectations of gene content from hundreds of species, to gauge completeness of rapidly accumulating genomic data and satisfy an Iberian's quest for quality - "Busco calidad/qualidade".

    • Address of the bookmark: http://busco.ezlab.org/

    ]]>     Anjana