sed -n '1~4s/^@/>/p;2~4p' file.fastq >file.fasta
sed '/^@/!d;s//>/;N' file.fastq >file.fasta
perl -pe '/^>/ ? print "\n" : chomp' multi-line.fasta >single-line.fasta
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < multi-line.fasta >single-line.fasta
perl -pe 'chomp unless /^>/' multi-line.fasta >single-line.fasta
awk '/^>/ { if(NR>1) print ""; printf("%s\n",$0); next; } { printf("%s",$0);} END {printf("\n");}' < multi-line.fasta >single-line.fasta
awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}' < multi-line.fasta >single-line.fasta
grep -A1 -f list_to_filter contigs.fasta >rm_contigs.fasta
grep -v -f rm_contigs.fasta contigs.fasta >output.fasta
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > out.fa
sed -E 's/("([^"]*)")?,/\2\t/g' file.csv >> file.tsv
cat file.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > file.fastq
find . -name "*.gff" -type f -exec cp {} ./. \;
split -d -a1 -b 10M --additional-suffix=.tsv metadata.tsv metadata
split -d -a1 -b 10M --additional-suffix=.fna seq.fna seq
awk '{s++}END{print s/4}' file.fastq
zcat file.fastq.gz | echo $((`wc -l`/4))
grep ">" file.fasta -c
grep ">" file.fasta | wc -l
grep "@" file.fastq -c
grep "@" file.fastq | wc -l
for i in *NAME*; do mv $i ${i/NAME/NEW_NAME}; done;
sed -r ‘s/\s+//g’
sed 's/[a-z]/\U&/g'
sed 's/[A-Z]/\L&/g'
sed 's/^[ ]*\([^ ]*\) /\1\t/' file.txt >New_file.txt
samtools view -S -f 4 file.bam >file_unmapped.sam
samtools view -S -F 4 file.sam >file_mapped.sam
samtools view -b -f 4 file.bam >file_unmapped.bam
samtools view -b -F 4 file.bam >file_mapped.bam
samtools fastq file.bam >file.fastq
bowtie2-build database.fa db
bowtie2 -p number of threads -x db -1 R1.fastq -2 R2.fastq -S global.sam --very-sensitive
bowtie2 -p number of threads -x db -q R1.fastq -S global.sam --very-sensitive
bowtie2 -p number of threads -x db -1 1.fastq -2 2.fastq -S local.sam --very-sensitive-local
bowtie2 -p number of threads -x db -q R1.fastq -S local.sam --very-sensitive-local`
mafft --localpair --maxiterate 1000 --clustalout file.fasta >file_local.clust
mafft --globalpair --maxiterate 1000 --clustalout file.fasta >file_global.clust
iqtree2 -s file_local.clust -st PRO -m TEST -bb 1000 -alrt 1000
iqtree2 -s file_local.clust -st DNA -m TEST -bb 1000 -alrt 1000
tree_annotator.py annotation.csv treefile output
The point-of-contact for this project is Dr. Richard Allen White III.
If you have any questions or feedback, please feel free to get in touch by email.
Dr. Richard Allen White III - [email protected] or [email protected]
Or open an issue.