<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37785?offset=510 https://bioinformaticsonline.com/bookmarks/view/28835/a5-miseq Thu, 18 Aug 2016 04:05:23 -0500 https://bioinformaticsonline.com/bookmarks/view/28835/a5-miseq <![CDATA[A5-miseq]]> _A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_.

Point to note:

There are many situations where A5-miseq is not the right tool for the job. In order to produce accurate results, A5-miseq requires Illumina data with certain characteristics. A5-miseq will likely not work well with Illumina reads shorter than around 80nt, or reads where the base qualities are low in all or most reads before 60nt. A5-miseq assumes it is assembling homozygous haploid genomes. Use a different assembler for metagenomes and heterozygous diploid or polyploid organisms. Use a different assembler if a tool like FastQC reports your data quality is dubious. You have been warned! Datasets consisting solely of unpaired reads are not currently supported.

Address of the bookmark: https://sourceforge.net/projects/ngopt/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29018/crossmap Mon, 05 Sep 2016 04:07:38 -0500 https://bioinformaticsonline.com/bookmarks/view/29018/crossmap <![CDATA[CrossMap]]>
  • CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).
  • It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.
  • CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.
  • We do not recommend using CrossMap to convert genome coordinates between species.

    • Address of the bookmark: http://crossmap.sourceforge.net/

    ]]>     Abhimanyu Singh