ARPIT MATHUR

@mberacochea I ran the following command : nextflow run virify.nf --illumina *R1.fastq.gz --output /home/arpit/same_Karishma_data_for_virify/ -profile local,docker --viphog true Nextflow-version: 21.10.6

@colindaven Thank you.

hi @colindaven actually I am using direct run_Wochenende.py on my Paired end FASTQ files. and I did not kept any path for alignerboost in the config file..... but it the...

thanks @colindaven . great tool by the way.

@colindaven will try

@colindaven yes trimming stopped after commenting 1541 to 1548 lines . thanks

@pmenzel yes. so these results are after wet lab negative template control data removal. Now question comes of false hits computationally. which is tough to decipher. False fastq files with...

I have ref fasta file as: >NZ_CP014581.1 AGCCGGTCGCCAACTTCAGCTCTCGTACATCCGGAGTCCAGCAGCGAGACGATCAGCTCC TGATCCGTTGTTATGACGCCGTCCGATTCACACTTTCGCATGCGAAATTTTACTCACTGT TCGACCGTACTGTAATTTTGTACGGAGTGCGCGCAGCGGCGCAGATATGAAAGACCTTCC GACTGCAGCAGTCCTGTCCATCCGGACCAGAAGGGCCGTCGTTCCCGCTCGACTCTACTT GACCAAGCCGGGCCTGACTCGCGGCGTCAGCAGCCACGAAACCTCGCCTTTCGGGCACTT CGAACGCACTCAAACACGAGCGATTCTAGCCGAACCACGTAGCCCGATCCAGGGGGATAT CGGACTTATTTCGCACCATCTATTGACCGTCAACATTTCTAATAATAATATCCGTTGCAC GTGACCACACGTCACCCATCAAAAATCAATGGACCGTCAATAACCGGAGCGTCTCATGTC CAACACCGTGCAATCGCGCATCTACCAGGCCCTTACCGAACTGATTCCGAATCTTGGAAA My taxid file is like A00001.1 10641 A00002.1 9913 A00003.1 9913 A00004.1 32630 A00005.1...

**Do the taxid file can't contain any other taxid which is not present in the reference.fasta ?**

@shenwei356 Can you provide kmcp indexed file and its database (.fna) file for bacterial identification ? my data is paried end cell free DNA fastq data.