runDrap 3rd party tools
| Process (step name) | Package | Version | Default command |
|---|---|---|---|
| Pre-processing (preprocess) |
parallel | 20141022 | parallel --joblog <logfile> -j %d -N %d <cmd> ::: <input_files> |
| trim_galore | 0.4.0 | trim_galore --gzip --no_report_file --length %d --output_dir <outdir> --quality 10 --stringency 3 --paired <R1.fq> <R2.fq> | |
| fastq_illumina_filter | 0.1 | fastq_illumina_filter -N | |
| Trinity | 2.4.0 | insilico_read_normalization.pl --seqType fq --JM %dG --CPU %d --output tmp_norm --max_cov 50 --pairs_together --PARALLEL_STATS --left <R1.fq> --right <R2.fq> | |
| Khmer | 2.0 | interleave-reads.py <R1.fq> <R2.fq> | |
| normalize-by-median.py -M %d --output - - | |||
| split-paired-reads.py -1 <R1.fq> -2 <R2.fq> | |||
| DBG assembly (dbg) |
Trinity | 2.4.0 | Trinity --no_cleanup --seqType fq --max_memory %dG --bflyHeapSpaceMax 4G --CPU %d --output <outdir>--no_normalize_reads --left <R1.fq> --right <R2.fq> |
| Velvet | 1.2.07 | velveth <outdir> 27 -shortPaired -fastq - -noHash | |
| velveth <outdir> <kmer> -strand_specific -reuse_Sequences | |||
| velvetg <outdir> -read_trkg yes -min_contig_lgth 100 -cov_cutoff 4 | |||
| Oases | 0.2.06 | oases <outdir> -cov_cutoff 4 | |
| DBG cleaning (merge) |
seqclean | 20110222 | seqclean <input.fa> -o <output.fa> |
| cdbyank -l <input.cidx> | |||
| NCBI Blast+ | 2.2.29 | blastn -query <input.fa> -subject <input.fa> -strand both -task megablast -dust no | |
| Inclusion removing (clustering) |
cd-hit | 4.6 | cd-hit-est -i <input.fa> -o <outdir> -M 0 -d 0 -c 0.98 |
| cd-hit -i <input.fa> -o <outdir> -M 0 -d 0 -c 0.90 -g 1 | |||
| OLC assembly (asm) |
tgicl | 2.1 | tgicl -F <input.fa> -l 60 -p 96 -s 100000 |
| Cleaning (post_asm) |
TransDecoder | 2.0.1 | TransDecoder.LongOrfs -t <input.fa> |
| TransDecoder.Predict -t <input.fa> | |||
| bedtools | 2.22.1 | bedtools merge -c 4 -o distinct -i - | |
| NCBI tools | 6.1 | vecscreen -i <input.fa> -d <database.fa> -f 3 | |
| EMBOSS | 6.4.0.0 | getorf -auto -filter | |
| Editing by reads alignment (rmbt_editing) |
bwa | 0.7.12 | bwa [aln|sampe|samse] |
| STAR | 2.4.0i | STAR --genomeDir <dir> --readFilesIn <R1.fq> <R2.fq> --alignIntronMin 10 --alignIntronMax 25000 --outFilterMultimapNmax 10000 | |
| samtools | 1.1 | samtools [mpileup|sort|index|flagstat|view|merge|faidx] | |
| Filtering by reads alignment (rmbt_filtering) |
eXpress | 1.5.1 | express --no-update-check --no-bias-correct --logtostderr --output-dir <outdir> <reference.fa> <input.bam> |
| Scoring (postprocess) |
TransRate | 1.0.1 | transrate --assembly=<input.fa> --left=<R1.fq> --right=<R2.fq> --threads=%d --output=<outdir> |
| Reference alignment (reference) |
Exonerate | 2.2.0 | exonerate --percent 50 --verbose 0 --showalignment no --showvulgar no <queries.fa> <targets.fa> |
| Blat | BlatSuite v34 | blat <targets.fa> <queries.fa> -noHead <output.psl> |