NGS Bioinformatics / Toolkit to assist overlapping paired-end reads merging
Development script not for production
check_merge will analyze a set of at least 2 output of a pair end merger (e.g. FLASH and VSEARCH), together with the unmerged reads, allowing to check the alignment and the quality scores produced.
Script that produces the merged files starting from the FASTQ pairs in the datasets directory.
Requires merging tools (namely flash, NGmerge, vsearch and optionally usearch)
to be available, or will attempt to install them via conda.
Will check an input sequence in FASTA or FASTQ format and detect the hypervariable regions of the reference (E. coli) 16S. If the input file contains more
than one sequence it will output the prediction for all of them, and since this can be slow (and useless) it can be avoided with -m INT switch
(maximum number of sequences to parse). Output can be in JSON format with (-j).
The JSON report has an "input_seqs" section, with the alignment read per read, and a "global_seqs" summary with the ratio (0-1) of sequences reported to cover a region.
{
"input_seqs" : {
"M02007:34:000000000-AK48W:1:1101:15713:1758" : {
"detected_regions" : "V3,V4",
"regions" : {
"V4" : 100,
"V3" : 98.47
},
"align_score" : 220.9
},
"M02007:34:000000000-AK48W:1:1101:17706:1679" : {
"align_score" : 263.1,
"regions" : {
"V4" : 100,
"V3" : 98.47
},
"detected_regions" : "V3,V4"
},
"M02007:34:000000000-AK48W:1:1101:11681:1769" : {
"detected_regions" : "V3,V4",
"regions" : {
"V3" : 98.47,
"V4" : 100
},
"align_score" : 210.5
}
},
"global_seqs" : {
"hit_ratios" : {
"V4" : 1,
"V3" : 1
}
}
}
the datasets directory contains Illumina paired end sequences obtained from: whole genome sequencing, 16S amplicon sequencing, ITS amplicon sequencing.