BOL

#Convert #FASTQ to FASTA and set bases of #quality lower than 20 to N $ seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta

#CheckM provides a set of tools for #assessing the #quality of #genomes recovered from isolates, single cells, or #metagenomes. http://ecogenomics.github.io/CheckM/

reformat.sh in=reads.fq out=highQuality.fq maq=16 (that will throw away all reads with average quality below 16) #Filter #BBMap #Quality

Reads QC http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/01/introQC.pdf #Quality #Reads #NGS