<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44229?offset=400 https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins Mon, 17 Aug 2020 05:25:10 -0500 https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins <![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]> SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

  1. Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
  2. Co-assembly of a large number of metagenomes via merging of individual metagenomes
  3. Includes binning and bin checking, for retrieving individual genomes
  4. The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
  5. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
  6. Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads Sun, 14 Mar 2021 09:42:47 -0500 https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads <![CDATA[AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads]]> AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

]]> Rahul Nayak https://bioinformaticsonline.com/pages/view/43728/short-read-assembly-using-spades Mon, 31 Jan 2022 07:18:16 -0600 https://bioinformaticsonline.com/pages/view/43728/short-read-assembly-using-spades <![CDATA[Short-read assembly using Spades !]]> If we only had Illumina reads, we could also assemble these using the tool Spades.

You can try this here, or try it later on your own data.

Get data

We will use the same Illumina data as we used above:

  • illumina_R1.fastq.gz: the Illumina forward reads
  • illumina_R2.fastq.gz: the Illumina reverse reads

Assemble

Run Spades:

spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina
  • -1 is input file of forward reads
  • -2 is input file of reverse reads
  • --careful minimizes mismatches and short indels
  • --cov-cutoff auto computes the coverage threshold (rather than the default setting, “off”)
  • -o is the output directory

Results

Move into the output directory and look at the contigs:

infoseq contigs.fasta
]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines Wed, 15 Jun 2016 17:18:36 -0500 https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines <![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]> LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.

Publication:

  • L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.

Download:

Address of the bookmark: https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/

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