tick_surveillance - v2.0.6

This release contains all updates from the latest stenglein-lab/tick_surveillance version 2.0.6

Full list of updates can be found here

Key updates: 1. Pipeline updated from DSL1 to DSL2 2. User instruction updated 3. Bug fixes 1. FastQC and Trimmed FastQC reports to results directory
2. When a target is mapped to multiple reporting columns, use a semicolon instead of a comma as the delimiter because comma was messing up csv output
3. Fixed logic for assigning contributing species names to names-type columns in surveillance report. Also improved comments in code and some variable name
4. Cutadapt: Modified so primers are trimmed all at once instead of separately. Ensures reads are only trimmed for primers once before they are passed to next step 4. Arguments added to improve customization:

| Workflow Step | Argument | Default |
|-----------------:|----------------:|---------------| | Cutadapt | --basecallqualitylimit | 18,18 | | DADA2 | --dada2MaxN | 0 | | DADA2 | --dada2maxEE | 2 | | DADA2 | --dada2MaxN | 0 | | DADA2 | --dada2truncQ | 2 | | DADA2 | --dada2trimRight | 0 | | DADA2 | --dada2minreads | 10 | | DADA2 | --dada2minoverlap | 12 | | DADA2 | --dada2maxmismatch | 0 | | BLAST report generation | --filterunassigned_seq | Borrelia,Borreliella,Babesia,Anaplasma,Ehrlichia |

- Groovy
Published by vir5 8 months ago

tick_surveillance - v1.0.6

This release contains all updates from the latest stenglein-lab/tick_surveillance version on 5/19/23

- Groovy
Published by vir5 almost 3 years ago

tick_surveillance - v1.0.5

This release includes the pipeline code from stengelin-lab/tick_surveillance v1.0.5

- Groovy
Published by vir5 about 3 years ago