NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing

• fastp

  9 1,768 4.7 C++

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  

1) QC the data with fastp. This'll trim out adapters and toss reads that are poor quality.

• bowtie2

  2 618 7.6 C++

  A fast and sensitive gapped read aligner

2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).

• InfluxDB

  www.influxdata.com sponsored

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• CHM13

  13 859 4.9

  The complete sequence of a human genome

  

2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).

• kraken2

  7 658 5.1 C++

  The second version of the Kraken taxonomic sequence classification system

3) Use Kraken2 to classify remaining reads. I'd start with the standard database.

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