FLOW

In positive psychology, flow, also known as the zone, is the mental state of operation in which a person performing an activity is fully immersed in a feeling of energized focus, full involvement, and enjoyment in the process of the activity. In essence, flow is characterized by complete absorption in what one does, and a resulting loss in one’s sense of space and time.

​ Mihály Csíkszentmihályi

Aspera

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'/c/Users/Lyole/AppData/Local/Programs/Aspera/Aspera Connect/bin/ascp.exe' -k 1 -QT -l 100M -i ~/etc/asperaweb_id_dsa.openssh -T anonftp@ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByStudy/sra/SRP/SRP075/SRP075747/
$ ascp -T -l 200M -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \
  --host=ftp-private.ncbi.nlm.nih.gov --user=anonftp --mode=recv \
  /sra/sra-instant/reads/ByRun/sra/ERR/ERR105/ERR105009/ERR105009.sra ./
$ ascp -T -l 200M -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \
  anonftp@ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/ERR/ERR105/ERR105009/ERR105009.sra ./

$ ascp -T -l 200M -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \
  --host=fasp.sra.ebi.ac.uk --user=era-fasp --mode=recv \
  /vol1/fastq/ERR105/ERR105009/ERR105009_1.fastq.gz ./
$ ascp -T -l 200M -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh \
  era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/ERR105/ERR105009/ERR105009_1.fastq.gz ./

SRA Toolkit

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# Converts data to fastq , fasta format ,gzipped and so on
#pair-end
fastq-dump --gzip --split-3 *.sra

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc

Fastqc

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/

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fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN

Trimmomatic

http://www.usadellab.org/cms/index.php?page=trimmomatic

MultiQC

http://multiqc.info/

HISAT2

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# extract_exons.py
# extract_splice_sites.py
# extract_snps.py
# hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
#e.g.

hisat2-build -p 4 genome.fa --snp genome.snp --ss genome.ss --exon genome.exon genome_snp_tran

hisat2 -p 16 -x ./path/to/genome_tran -1 SRR*_1.fastq -2 SRR*_2.fastq –S SRR*.sam

http://ccb.jhu.edu/software/hisat2/manual.shtml

STAR

SAMtools

QC

HTSeq