Tassy J. Bazile

Do we need to build an index for each DB prior to run kakrenuniq for hierachical classification? krakenuniq --dbDB1 --db DB2 --db DB3 Is this the way we build it...

Installing bactopia

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Hello Robert, In installing bactopia, is there any step that precedes the databases downloading? Actually, after conda activate bactopia ---? bactopia datasets (isn't moving any further) Thanks! TJ

[INFO][Launcher]biostar139647 Exited with failure (-1)

1

### Verify Module installed in cluster java/1.8.0_31 3) jvarkit/20180405 ### Subject of the issue I want to convert a fasta alignment into bam command used: biostar139647 aln_dir/lp_allstrains03.aln -o aln_dir/lp_allstrains03.bam --samoutputformat...

snippy core took isolate as ref

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Hi Seeman I ran snippy on mutliple isolates with the input.tab snippy-multi input.tab --ref ../gubbins_dir/ref_seq_dir/GCF_001600975_1_ASM160097v1.fasta --cpus 16 > runme.sh When checked the file runme.sh, I noticed one of my isolates...

Hi Fukasawa, Is it not necessary to run fastqc on the trimmed reads? I would like check if the quality has improved after trimming from longQC? (I tried fastqc, but...

Adaptor trimming

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Hi Yoshinori, I am trying to trim adaptors from ONT reads: Do we just use the flags --adapter_5 ADP5 --adapter_3 ADP3? I have used this: for s in $(cat samples_ont.txt);do...

Getting Assembly metrics

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Hi Iskatz, I need to compute assembly metrics, including coverage. My input data files are single-end fastq and the genome assembly fasta . In the documentation, paired-end reads must be...

samtools errors

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I was running midas as a module, module load midas /1.3.2 I encountered this error Error: could not execute samtools binary: samtools (exited with error code 127) To solve this...