Tools for long reads
In this page are listed all analyses and bioinformatic tools available for long reads in CIS. Long reads can be processed only with tools that are specifically designed to manage them.
Analyses for long reads from Oxford Nanopore
| Analysis | Tool | Notes |
|---|---|---|
| 1PP_filtering__minimap2 | minimap2 | only for reads from Nanopore apparatus |
| 1PP_hostdepl__minimap2 | minimap2 | only for reads from Nanopore apparatus |
| 1PP_trimming__chopper | chopper | only for reads from Nanopore apparatus |
| 2AS_denovo__flye | Flye | only for reads from Nanopore apparatus |
| 2AS_hybrid__unicycler | Unicycler | for hybrid assembly of Illumina short reads and Nanopore long reads |
| 2AS_mapping__medaka | Medaka | only for reads from Nanopore apparatus |
| 3TX_class__centrifuge | Centrifuge | only for reads from Nanopore apparatus |
Analyses for long reads from Thermofisher IonTorrent
| Analysis | Tool | Notes |
|---|---|---|
| 1PP_trimming__fastp | fastp | only for reads from IonTorrent apparatus |
| 1PP_trimming__trimmomatic | trimmomatic | for long reads from IonTorrent and paired-end short reads |
| 2AS_denovo__plasmidspades | plasmidSPAdes | only for reads from IonTorrent apparatus (assembly of plasmid sequences) |
| 2AS_denovo__shovill | shovill | for long reads from IonTorrent and paired-end short reads |
| 2AS_denovo__spades | SPAdes | for long reads from IonTorrent and paired-end short reads |
| 2AS_mapping__bowtie | bowtie | for long reads from IonTorrent and paired-end short reads |
| 2AS_mapping__ivar | iVar | for long reads from IonTorrent and paired-end short reads |
| 2AS_mapping__snippy | snippy | for long reads from IonTorrent and paired-end short reads |
| 3TX_class__confindr | ConFindr | for long reads from IonTorrent and paired-end short reads |
| 3TX_class__kraken | kraken | for long reads from IonTorrent and paired-end short reads |
| 3TX_class__kraken2 | kraken2 | for long reads from IonTorrent and paired-end short reads |
| 3TX_species__mash | Mash | for long reads from IonTorrent and paired-end short reads |
| 4AN_AMR__resfinder | resfinder | for long reads from IonTorrent and paired-end short reads |
