<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44371?offset=500 https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats Thu, 07 Mar 2019 21:13:06 -0600 https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats <![CDATA[HipSTR: Haplotype inference and phasing for Short Tandem Repeats]]> HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by:

  1. Learning locus-specific PCR stutter models using an EM algorithm
  2. Mining candidate STR alleles from population-scale sequencing data
  3. Employing a specialized hidden Markov model to align reads to candidate alleles while accounting for STR artifacts
  4. Utilizing phased SNP haplotypes to genotype and phase STRs

Address of the bookmark: https://github.com/tfwillems/HipSTR

]]> BioJoker https://bioinformaticsonline.com/file/view/43732/spades-tutorial-pdf Tue, 01 Feb 2022 04:56:43 -0600 https://bioinformaticsonline.com/file/view/43732/spades-tutorial-pdf <![CDATA[Spades tutorial PDF]]> SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets. 

]]> Abhimanyu Singh