{"repo":"nf-core/kmermaid","free":true,"listed":false,"github":"https://github.com/nf-core/kmermaid","clone":"git clone https://github.com/nf-core/kmermaid.git","description":"k-mer similarity analysis pipeline","language":"Nextflow","stars":24,"topics":["nf-core","workflow","pipeline","nextflow","kmer","k-mer","kmer-frequency-count","kmer-counting"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/kmermaid is a bioinformatics pipeline that performs comparative analysis of \\ omes using k-mer based methods. It supports various reference and sequencing input formats, and provides statistics files along with a MultiQC report as output. It provides pre-processing methods for reads and alignments. In the outline below, every step except for the main analysis is optional and might be input-dependent. Optional – BAM preprocessing 1. Extract BAM from 10X archive ( tar ) 2. Extract FASTQ reads ( samtools ) 3. Split reads per cell ( grep ) 4. Count UMIs per cell ( pbtk ) 5. Download SRA experiment () [optional] Optional – read preprocessing 6. Trim reads ( fastp ) 7. Read QC ( FastQC ) 8. Remove rRNA ( sortmerna ) 9. Translate to protein ( orpheum ) k-mer analysis per method 10. Create sketch 11. Calculate distances 12. Present the results ( MultiQC ) [!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data. Usage With a samples.csv file With R1, R2 read pairs With SRA ids With fasta files With bam file With split kmer Credits nf-core/kmermaid was originally written by Olga Botvinnik. The DSL2 port is done by Igor Trujnara. We thank the following people for their extensive assistance in the development of this pipeline: Contributions and Support If you would like to contribute to this pipeline, please see the contributing guide","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/kmermaid/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}