Created
January 18, 2023 09:11
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| Aligning > 1MB long sequences (e.g. long DNA sequences) can take quite long with Needleman Wunsch | |
| An alternative is using the BWA: | |
| http://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf | |
| #1 Create index: | |
| ../bwa-0.7.17/bwa index -p index_path -a bwtsw dna_reference.fasta | |
| ./bwa-0.7.17/bwa mem -t 16 index_path dna_of_interest.fasta | ./samtools-1.16.1/samtools sort -o output.bam - | |
BETTER ALTERNATIVE:
use minimap2
../minimap2-2.24_x64-linux/minimap2 -ax asm5 ../reference.fasta ../target.fasta > approx_alignment.paf
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Extracting the alignment:
https://bioinformatics.stackexchange.com/questions/7048/how-to-get-fasta-alignment-file-from-sam-bam-file