xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-08 17:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

phasing

Browse Source
This commit is contained in:
Haoyu Cheng
2019-09-02 10:30:14 -04:00
parent 3c0c201cdf
commit d5327fe9ee
15 changed files with 3396 additions and 656 deletions
Download Patch File Download Diff File Expand all files Collapse all files
debug_assembly.sh
+17
View File
@@ -0,0 +1,17 @@
#!/bin/bash
# My first script
if [ $# -eq 1 ]
then
echo "../minimap2/minimap2 -ax asm20 -t 32 ../minimap2/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz "$1" >"$1".sam"
../minimap2/minimap2 -ax asm20 -t 32 ../minimap2/Homo_sapiens.GRCh38.dna.primary_assembly.fa $1 >$1.sam
echo "samtools view -Sb "$1".sam >"$1".bam"
samtools view -Sb $1.sam >$1.bam
echo "samtools sort "$1".bam sort_"$1
samtools sort $1.bam sort_$1
echo "rm sort_"$1".bam.bai"
rm sort_$1.bam.bai
echo "samtools index sort_"$1".bam"
samtools index sort_$1.bam
else
echo "debug_assembly.sh intput.fa"
fi