seqfu merge

A tool to naively merge paired end reads preserving the quality of the forward read.

Usage: merge [options] -1 File_R1

  Options:
  -1, --R1 FILE                First paired-end file
  -2, --R2 FILE                Second paired-end file, can be automatically inferred  
  -i, --minid FLOAT            Minimum identity [default: 0.80]
  -m, --minlen INT             Minimum overlap [default: 20]
  --accepted-identity FLOAT    Accept fusion when identity is above FLOAT [default: 0.96]
  -v, --verbose                Print verbose messages
  -h, --help                   Show this help

Merging reads

There are several tools to merge overlapping reads, and some are better than others. In particular if we use tools that correcly interpret the Phred quality scores, then tools like USEARCH and VSEARCH are correcly recalibrating the quality of the overlapping bases.

Some tools, however, are expeting quality scores that are more likely produced by a sequencing tool. This experimental module of SeqFu joins the reads in a different way: takes the forward read as is, and extends it with the (reverse complemented) missing part taken from the R2.

Potential uses

This tool can be used to estimate the overlapping size or the "mergeability" of reads before using the tools of choice.

For example:

seqfu merge -1 reads_R1.fq | seqfu head -n 200 | seqfu stats -n

Output

The merged reads are printed to the standard output.

Also this is somehow unusual compared with most mergin tools, but allows streaming which is a core feature in SeqFu tools.