Commit d08b1899 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

Update output.md

parent 21c9ebdf
......@@ -44,12 +44,12 @@ The `results/` directory contains a sub-directory for each step launched:
| File or directory/ | Description |
| ----------------------- | --------------------------------------- |
| `SAMPLE_NAME_metaspades/SAMPLE_NAME_spades_log.txt` | metaspades logs. Only if `--assembly "metaspades"` is used.|
| `SAMPLE_NAME_metaspades/params.txt` | metaspades command line parameters used for the analysis. Only if `--assembly "metaspades"` is used.|
| `SAMPLE_NAME_metaspades/SAMPLE_NAME_scaffolds.fasta` | metaspades assembly: nucleotide sequence of contigs. Only if `--assembly "metaspades"` is used.|
| `SAMPLE_NAME_megahit/SAMPLE_NAME.log` | megahit logs. Only if `--assembly "megahit"` is used.|
| `SAMPLE_NAME_megahit/options.json` | megahit options used for the analysis. Only if `--assembly "megahit"` is used.|
| `SAMPLE_NAME_megahit/SAMPLE_NAME.contigs.fa` | megahit assembly: nucleotide sequence of contigs. Only if `--assembly "megahit"` is used.|
| `metaspades/SAMPLE_NAME.log` | metaspades logs. Only if `--assembly "metaspades"` is used.|
| `metaspades/SAMPLE_NAME.params.txt` | metaspades command line parameters used for the analysis. Only if `--assembly "metaspades"` is used.|
| `metaspades/SAMPLE_NAME.contigs.fa` | metaspades assembly: nucleotide sequence of contigs. Only if `--assembly "metaspades"` is used.|
| `megahit/SAMPLE_NAME.log` | megahit logs. Only if `--assembly "megahit"` is used.|
| `megahit/SAMPLE_NAME.params.txt` | megahit options used for the analysis. Only if `--assembly "megahit"` is used.|
| `megahit/SAMPLE_NAME.contigs.fa` | megahit assembly: nucleotide sequence of contigs. Only if `--assembly "megahit"` is used.|
| `SAMPLE_NAME_all_contigs_QC/` | Contains metaQUAST quality control files of contigs. |
| `SAMPLE_NAME_R{1,2}_dedup.fastq.gz` | Deduplicated reads (R1 and R2 files) for SAMPLE_NAME sample. |
| `logs/` | Contains `SAMPLE_NAME.count_reads_on_contigs.flagstat`, `SAMPLE_NAME.count_reads_on_contigs.idxstats` and `SAMPLE_NAME_dedup_R{1,2}.nb_bases` files for each sample, generated after deduplication of reads. `SAMPLE_NAME.count_reads_on_contigs.flagstat` and `SAMPLE_NAME.count_reads_on_contigs.idxstats` are respectively the results of samtools flagstat (see informations [here](http://www.htslib.org/doc/samtools-flagstat.html)) and samtools idxstats (see description [here](http://www.htslib.org/doc/samtools-idxstats.html)), `SAMPLE_NAME_R{1,2}.nb_bases` corresponds to the number of nucleotides into deduplicated R1 and R2 files. |
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