Program,Command line,Dataset
fastqc,fastqc -t 2 --noextract $read_in -o $fastqc_report,"1,2,3,4"
prinseq,"prinseq-lite -fastq $read_in -out_good stdout -out_bad null -qual_noscale -graph_data $read_in.stat -graph_stats ld,gc,qd,ns,pt,ts,aq,de,sc,dn -no_qual_header -trim_qual_window 1 -trim_qual_step 1 -trim_qual_right 20 -lc_method dust -lc_threshold 32 -trim_tail_right 6 -min_qal_mean 20 > $read_out","1,2,3,4"
trinity,Trinity --left $reads1 --right $reads2 --output $trin_out --max_reads_per_graph 2000000 --seqType fq --JM 40G --CPU 16 --inchworm_cpu 16 --bflyCPU 7 --bflyHeapSpaceMax 8G --min_iso_ratio 0.05 --max_number_of_paths_per_node 10 --glue_factor 0.05 --min_glue 2 --path_reinforcement_distance 75 --group_pairs_distance 500 --min_kmer_cov 1 --min_contig_length 100,"2,3,4"
trinity,Trinity --SS_lib_type RF --left $reads1 --right $reads2 --output $trin_out --max_reads_per_graph 2000000 --seqType fq --JM 40G --CPU 16 --inchworm_cpu 16 --bflyCPU 7 --bflyHeapSpaceMax 8G --min_iso_ratio 0.05 --max_number_of_paths_per_node 10 --glue_factor 0.05 --min_glue 2 --path_reinforcement_distance 75 --group_pairs_distance 500 --min_kmer_cov 1 --min_contig_length 200,1
bowtie2,bowtie2-build $transcripts $index,"1,2,3,4"
bowtie2,bowtie2 -x $index -1 $reads1 -2 $reads2 -U $unpaired_reads --maxins 500 --minins 0 --end-to-end --sensitive,"1,2,3,4"
blast,blastx -query $query -db $db -out $out -evalue 1e-6 -num_threads 16 -outfmt 5 -max_target_seqs 100,"1,2,3,4"
hmmer,hmmscan -o $output --tblout $file.out.tab --cpu 16 PfamA.hmm $transcripts,"1,2,3,4"
blast2go,java -cp *:ext/*: es.blast2go.prog.B2GAnnotPipe -in $xml_in -out $out_b2go -prop $b2gPipe.properties_new -v -annot -dat -annex,"1,2,3,4"