Skip to content

docs: shuffling page gives the measured aligner memory effect (#870) #873

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
joshfactorial wants to merge 1 commit into
base: develop
Choose a base branch
from
Open

docs: shuffling page gives the measured aligner memory effect (#870) #873

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion docs-site/src/gen-reads/fastq-shuffling.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,9 @@
real sequencer's FASTQ is in effectively random order. Variant calling does not depend on this,
since the BAM is coordinate-sorted before calling. Tools that read the FASTQ in batches,
aligners in particular, do see the difference: a batch can be filled entirely with reads from
one region, such as a long satellite array. Shuffle before aligning if that matters to you.
one region, such as a long satellite array. Measured on a 21x simulation of T2T-CHM13 (#870),
bwa-mem2 peaked at 166 GB on the reads as written and at 90 GB on the same reads shuffled,
with the same alignments either way. Shuffle before aligning a large genome.
#870 tracks shuffling in `eidolon` itself.

With `seqkit`, shuffle each mate separately **with the same seed**. seqkit has no paired mode,
Expand Down
Loading