-d <string> displays the alien oligonucleotide sequences corresponding to the specified key
word(s); see option -a for the list of available key words
-q <int> quality score threshold; all bases with Phred score below this threshold are
-q <int> quality score threshold; all bases with Phred score below this threshold are
considered as non-confident (default: 15)
-l <int> minimum required length for a read (default: half the average read length)
-p <int> maximum allowed percentage of non-confident bases (as ruled by option -q) per
-p <int> maximum allowed percentage of non-confident bases (as ruled by option -q) per
read (default: 50)
-c <int> minimum allowed coverage depth for step 'L' or 'N' (default: 4)
-C <int> maximum allowed coverage depth for step 'R' or 'N' (default: 90)
-s <string> a sequence of tasks to be iteratively performed, each being defined by one of
-s <string> a sequence of tasks to be iteratively performed, each being defined by one of
the following uppercase characters:
C discarding [C]ontaminating reads (as ruled by option -A)
E correcting sequencing [E]rrors
...
...
@@ -199,7 +199,7 @@ Run _fqCleanER_ without option to read the following documentation:
<spanstyle="color:navy; font-size:1.1em;">**[T]**</span> Trimming and clipping (`-s T`) are performed using [_AlienTrimmer_](https://research.pasteur.fr/en/software/alientrimmer/)(Criscuolo and Brisse 2013). Clipping is carried out based on the specified alien oligonucleotides (option `-a`), where alien oligonucleotide sequences can be (i) set using precomputed standard library names, (ii) specified via user-defined FASTA-formatted file, or (iii) directly estimated from the input files using [_AlienDiscover_](https://gitlab.pasteur.fr/GIPhy/AlienDiscover)(option`-a AUTO`). When step T is run without setting option `-a`, clipping is carried out with the four homopolymers (`POLY`) as alien oligonucleotides. Trimming is carried out by deleting 5' and 3' regions containing many non-confident bases, where a base is considered as non-confident when its Phred score is lower than a Phred score threshold (set using option `-q`; default: 15). After trimming/clipping an HTS read, it can be discarded when the number of remaining bases is lower than a specified length threshold (option `-l`; default: half the average read length) or when the percentage of remaining non-confident bases is higher than another specified threshold (option `-p`; default: 50%). Note that when HTS read discarding breaks PE, singletons are written into dedicated output files ( _.S.fastq_ file extension).
