about weeSam command

Question

[jacobnix]

Hello everybody ,

I'm trying to use MetaVic Pipeline (Metagenomics without reference) but in the Assemble. sh script , they are using weeSAM command , I have tried to search this app or command weeSAM without success :

https://github.com/sejmodha/MetaViC/blob/master/Assemble.sh

some extract Assemble.sh shell script:

samtools view -b $3.sam > $3.bam

samtools sort -o $3_sorted.bam $3.bam samtools index $3_sorted.bam

weeSAMv1.1 -b $3_sorted.bam -out $3_weeSAM_out

Answer 1

[Sej Modha]

weeSAM is a custom script written by Joseph Hughes that is part of the MetaViC pipeline and available to download from https://github.com/josephhughes/Sequence-manipulation/blob/master/weeSAMv1.1

[jacobnix]

Sej thank you so much !! :D