<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/30090?offset=140 https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Fri, 24 Jan 2020 04:09:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40598/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. MitoZ is available from https://github.com/linzhi2013/MitoZ.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics Tue, 17 Mar 2020 06:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/41459/jcvipython-utility-libraries-on-genome-assembly-annotation-and-comparative-genomics <![CDATA[JCVI:Python utility libraries on genome assembly, annotation and comparative genomics]]> Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads Mon, 04 May 2020 02:04:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads <![CDATA[HASLR: a hybrid assembler which uses both second and third generation sequencing reads]]> HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/42267/hapsolo-an-optimization-approach-for-removing-secondary-haplotigs-during-diploid-genome-assembly-and-scaffolding Mon, 26 Oct 2020 21:23:36 -0500 https://bioinformaticsonline.com/bookmarks/view/42267/hapsolo-an-optimization-approach-for-removing-secondary-haplotigs-during-diploid-genome-assembly-and-scaffolding <![CDATA[HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.]]> Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

More at https://github.com/esolares/HapSolo

Address of the bookmark: https://github.com/esolares/HapSolo

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43057/hapsolo-an-optimization-approach-for-removing-secondary-haplotigs-during-diploid-genome-assembly-and-scaffolding Sat, 08 May 2021 21:25:00 -0500 https://bioinformaticsonline.com/bookmarks/view/43057/hapsolo-an-optimization-approach-for-removing-secondary-haplotigs-during-diploid-genome-assembly-and-scaffolding <![CDATA[HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding]]> HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. 

Address of the bookmark: https://github.com/esolares/HapSolo

]]> Jit 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/36239/scilifelab-tutorial-for-bioinformatics-analysis Tue, 17 Apr 2018 04:33:00 -0500 https://bioinformaticsonline.com/bookmarks/view/36239/scilifelab-tutorial-for-bioinformatics-analysis <![CDATA[SciLifeLab tutorial for bioinformatics analysis !]]> SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

Metagenomics Workshop

2015 November - Uppsala
2016 November - Uppsala
2017 November - Uppsala

Introduction to Bioinformatics Using NGS Data

2015 February - Uppsala 
2015 May - Gothenburg
2015 September - Uppsala
2015 November - Lund
2016 January - Uppsala
2016 April - Linköping
2016 September - Uppsala
2016 November - Umeå
2017 January - Uppsala
2017 May - Gothenburg
2017 September - Lund
2017 November - Uppsala
2018 February - Uppsala

Introduction to Genome Annotation

2015 April - Uppsala
2016 April - Uppsala
2017 April - Uppsala
2018 May - Uppsala

De Novo Genome Assembly

2016 November - Uppsala
2017 November - Uppsala

RNA-seq course

2015 October - Uppsala
2016 April - Uppsala
2016 October - Uppsala
2017 March - Uppsala
2017 November - Uppsala
RNAseq tutorials

R Programming Foundations for Life Scientists

2016 November - Uppsala
2017 Mars - Uppsala

Single cell RNA sequencing analysis

2017 October - Uppsala

Address of the bookmark: https://scilifelab.github.io/courses/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36880/jvarkit-java-utilities-for-bioinformatics Fri, 08 Jun 2018 09:31:55 -0500 https://bioinformaticsonline.com/bookmarks/view/36880/jvarkit-java-utilities-for-bioinformatics <![CDATA[Jvarkit : Java utilities for Bioinformatics]]> Address of the bookmark: http://lindenb.github.io/jvarkit/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44373/mitohifi-a-python-pipeline-for-mitochondrial-genome-assembly-from-pacbio-high-fidelity-reads Tue, 05 Sep 2023 07:31:35 -0500 https://bioinformaticsonline.com/bookmarks/view/44373/mitohifi-a-python-pipeline-for-mitochondrial-genome-assembly-from-pacbio-high-fidelity-reads <![CDATA[MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads]]> MitoHiFi v3.2 is a python pipeline distributed under MIT License !

MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-y 

Address of the bookmark: https://github.com/marcelauliano/MitoHiFi

]]> Abhi 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