From a0e4cbf80a376d70c5bb58993c0dcca853454277 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 17 Apr 2021 16:07:34 -0400 Subject: [PATCH] minor changes --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 507e256..4702cfa 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,16 @@ awk '/^S/{print ">"$2;print $3}' test.p_ctg.gfa > test.p_ctg.fa # get primary c # Assemble inbred/homozygous genomes (-l0 disables duplication purging) hifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2> CHM13.asm.log -# Assemble heterozygous with built-in duplication purging +# Assemble heterozygous genomes with built-in duplication purging hifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.fq.gz +# Hi-C phasing with paired-end short reads in two FASTQ files +hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz + # Trio binning assembly (requiring https://github.com/lh3/yak) yak count -b37 -t16 -o pat.yak <(cat pat_1.fq.gz pat_2.fq.gz) <(cat pat_1.fq.gz pat_2.fq.gz) yak count -b37 -t16 -o mat.yak <(cat mat_1.fq.gz mat_2.fq.gz) <(cat mat_1.fq.gz mat_2.fq.gz) hifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz - -# Hi-C phasing with paired-end short reads in two FASTQ files -hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz ``` ## Table of Contents @@ -91,7 +91,7 @@ At the first run, hifiasm saves corrected reads and overlaps to disk as `NA12878.asm.*.bin`. It reuses the saved results to avoid the time-consuming all-vs-all overlap calculation next time. You may specify `-i` to ignore precomputed overlaps and redo overlapping from raw reads. -You can also dump error corrected in FASTA and/or overlaps in PAF with +You can also dump error corrected reads in FASTA and read overlaps in PAF with ```sh hifiasm -o NA12878.asm -t 32 --write-paf --write-ec /dev/null ```