Carolina
  • About Me
  • Featured on
  • Pipelines
    Mapping and variant calling (short reads) Population SV calling Population mapping Nanopore assembly and var calling Population variant calling Whole genome alignment
  • Search
✕

    Population mapping pipeline is now available

    Posted on September 30, 2021

    The pipeline to map the reads from several samples to a (reference) genome is now available. As input it takes a .fasta file of a reference genome, and one or more paths to directories that contain reads. The pipeline will go through every subdirectory of the path you gave as... [Read More]
    Tags: snakemake pipeline bioinformatics mapping bwa population

    Population structural variant calling pipeline is now available

    Posted on September 22, 2021

    The pipeline to perform structural variant calling in a population using Smoove is now available. It also runs VEP and performs PCA. You can find the description here. There you can also find the tools that the pipeline uses and the output. The pipeline can be found here. [Read More]
    Tags: snakemake pipeline bioinformatics structural variance smoove vep

    How to fix smoove errors

    Posted on August 12, 2021

    In this post I will show how to solve some Smoove issues I came across. I’m using smoove v0.2.8 installed with conda. [Read More]
    Tags: bioinformatics smoove svtyper structural variance SR=0 bwa mem

    Mapping and variant calling pipeline is now available

    Posted on July 1, 2021

    The pipeline for mapping short reads and performing variant calling is now available. You can find a short description here. There you can also find the tools that the pipeline uses and the output. The pipeline can be found here. [Read More]
    Tags: snakemake pipeline bioinformatics mapping short reads variant calling freebayes

    How to run my pipelines

    Posted on June 23, 2021

    Most of my pipelines are created with Snakemake and use modules loaded from the HPC and tools installed with conda. [Read More]
    Tags: snakemake pipeline bioinformatics
    • ← Newer Posts
    • Older Posts →
    • GitHub
    • LinkedIn

    Carolina Pita Barros  •  2024

    Powered by Beautiful Jekyll