BWA MEM with merged paired-end reads and unmerged in the same run.

• samtools

  3 1,549 8.6 C

  Tools (written in C using htslib) for manipulating next-generation sequencing data

  

I don’t know about your first question, but for your second, use “bwa mem -p …” for smart pairing of an interleaved FASTQ/A with both paired end reads and singletons. BWA will recognize whether adjacent reads are paired if they have the same prefix (see here)

• 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.

  

Suggest a related project