This is a test version of Biostars. For the public version, visit https://www.biostars.org.
minimap2 cigar entry

Hi all,

I'd like to understand the CIGAR entry for minimap2 alignments. The numbers of cigar entries for a given read seems to not line up with the sequence...

Does anyone have an explanation of CIGAR entry for minimap2?

Thanks

sequencing genome alignment
• 3,315 views • link
updated by Biostar Biostar • written by zinderelly • zinderelly

This is for nanopore long read alignments.

• 0 views • link
written by zinderelly • zinderelly

Please add details (=data examples). Words alone often do not suffice.

• 0 views • link
written by ATpoint ATpoint

The minimap2 CIGAR structure is not special, it follows the SAM specifications.

• 0 views • link
written by WouterDeCoster WouterDeCoster

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Understanding Re-use of Query Sequences in Long Read Alignments
    written by Charles-Alexandre Roy • Charles-Alexandre Roy
    Hi all, I've been testing the alignment of some PacBio reads using `pbmm2` and `Minimap2` and observed a phenomenon that I can't make sense of. …
  • How can I find the position of a sequence in a fastq file
    written by pomodoro_sinensis • pomodoro_sinensis
    Hello, I have a fastq file with 4 lines per sequence. This is an example of one of the entries: @m54284U_200831_121835/3/ccs ATGGGTGGGCTGGCAGTAGCCAGGGACGATGGGCTCTTCTCTGGGGATCCCAACTGGTTTCCTAAGAAATCCAAGGAGAACCCTCGGAACTTCTCGGACAACCAGTTGCAAGAGGGCAAGAACGTGATTGGGTTGCAGATGGGCACCAACCGTGGAGCATCTCAGGCCGGCATGACCGGCTATGGGATGCCACGGCAGATCCTCTGATCATACTCTCTCTCCTTCCCCTGCCCTCCATGAATGGTTAATATATATGTATATATATGTTTTAGCAGACATTCCCTGAGAGCCCCTGGATTGCTGAACCCCCCTCTGCCAGGGTCCAGGCCAGCCTATCTTGTCACCACTGGCAGGGCCTGATAATTGCCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTGGGCTTACTAATGCATTCCTCCCCCCACATTATTCCCACAGTCTCAAGCACGTGGATTCTGCTGTAGTCGTACGCCGATGCGAAACATCGGCCACGTCGCTATTGCAGCGAGTAGATCGGAAGAGCACACGTCTGAACTCCA + 5555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 I …
  • Alignment Score (AS) tag in minimap2
    written by tim.booth • tim.booth
    Hi, I'm working with some SAM files generated by minimap2. The reads have been aligned to a spike-in reference so I'd like to use the …
  • Want to loop through list of BLAST objects in python
    written by westin.kosater • westin.kosater
    I performed a BLAST search with Biopython from a FASTA file with 92 entries (`goat.fasta`) from Bio.Blast import NCBIWWW from Bio.Blast import NCBIXML import pandas …
  • Randomising the content of a site in a nucleotide alignment without altering composition
    written by treesandthings • treesandthings
    Hi everyone, I have a DNA sequence alignment in a .fasta format that I'd like to read in using R, choose one of a given …
  • samtools mpileup output documentation
    written by bec • bec
    Hi, Can anyone provide me with a link to documentation giving an explanation for all of the samtools mpileup output sequence characters? (ie an explanation …
  • Splitting SAM/BAM alignments
    written by Zev.Kronenberg Zev.Kronenberg
    Greetings, I'm aligning large contigs to a reference genome. I'm hitting upper limit on the number of CIGAR operations (error below). Does anyone have a …
  • Is it possible to reconstruct alignment from CIGAR and MD strings alone?
    written by Lynxoid Lynxoid
    I have a SAM file with alignments and for each entry alignment, I want to reconstruct the alignment between the reference and the read based …
  • Tool to unmark duplicates
    written by Mark Ebbert Mark Ebbert
    Hi, I received some bams where duplicates were marked using Picard. I'd like to unmark all duplicate reads for a study we're doing. Does anyone …
  • Mapping Reads Back To Assembly Contigs
    written by David M David M
    <p>Does anyone know of a program which can efficiently map read data back to an assembly itself in a reasonable amount of time?</p> <p>I'd like …