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third_party_tools.html
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<!DOCTYPE html>
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<h1>runDrap 3rd party tools</h1>
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<div class="table-responsive">
<table class="table">
<thead>
<tr>
<th>Process (step name)</th>
<th>Package</th>
<th>Version</th>
<th>Default command</th>
</tr>
</thead>
<tbody>
<tr>
<td rowspan="7">Pre-processing<br>(preprocess)</td>
<td>parallel</td>
<td>20141022</td>
<td style="font-family: Courier New">parallel --joblog <logfile> -j %d -N %d <cmd> ::: <input_files></td>
</tr>
<tr>
<td>trim_galore</td>
<td>0.4.0</td>
<td style="font-family: Courier New">trim_galore --gzip --no_report_file --length %d --output_dir <outdir> --quality 10 --stringency 3 --paired <R1.fq> <R2.fq></td>
</tr>
<tr>
<td>fastq_illumina_filter</td>
<td>0.1</td>
<td style="font-family: Courier New">fastq_illumina_filter -N</td>
</tr>
<tr>
<td>Trinity</td>
<td>2.4.0</td>
<td style="font-family: Courier New">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></td>
</tr>
<tr>
<td rowspan="3">Khmer</td>
<td rowspan="3">2.0</td>
<td style="font-family: Courier New">interleave-reads.py <R1.fq> <R2.fq></td>
</tr>
<tr>
<td style="font-family: Courier New">normalize-by-median.py -M %d --output - -</td>
</tr>
<tr>
<td style="font-family: Courier New">split-paired-reads.py -1 <R1.fq> -2 <R2.fq></td>
</tr>
<tr>
<td rowspan="5">DBG assembly<br>(dbg)</td>
<td>Trinity</td>
<td>2.4.0</td>
<td style="font-family: Courier New">Trinity --no_cleanup --seqType fq --max_memory %dG --bflyHeapSpaceMax 4G --CPU %d --output <outdir>--no_normalize_reads --left <R1.fq> --right <R2.fq></td>
</tr>
<tr>
<td rowspan="3">Velvet</td>
<td rowspan="3">1.2.07</td>
<td style="font-family: Courier New">velveth <outdir> 27 -shortPaired -fastq - -noHash</td>
</tr>
<tr>
<td style="font-family: Courier New">velveth <outdir> <kmer> -strand_specific -reuse_Sequences</td>
</tr>
<tr>
<td style="font-family: Courier New">velvetg <outdir> -read_trkg yes -min_contig_lgth 100 -cov_cutoff 4</td>
</tr>
<tr>
<td>Oases</td>
<td>0.2.06</td>
<td style="font-family: Courier New">oases <outdir> -cov_cutoff 4</td>
</tr>
<tr>
<td rowspan="3">DBG cleaning<br>(merge)</td>
<td rowspan="2">seqclean</td>
<td rowspan="2">20110222</td>
<td style="font-family: Courier New">seqclean <input.fa> -o <output.fa></td>
</tr>
<tr>
<td style="font-family: Courier New">cdbyank -l <input.cidx></td>
</tr>
<tr>
<td>NCBI Blast+</td>
<td>2.2.29</td>
<td style="font-family: Courier New">blastn -query <input.fa> -subject <input.fa> -strand both -task megablast -dust no</td>
</tr>
<tr>
<td rowspan="2">Inclusion removing<br>(clustering)</td>
<td rowspan="2">cd-hit</td>
<td rowspan="2">4.6</td>
<td style="font-family: Courier New">cd-hit-est -i <input.fa> -o <outdir> -M 0 -d 0 -c 0.98</td>
</tr>
<tr>
<td style="font-family: Courier New">cd-hit -i <input.fa> -o <outdir> -M 0 -d 0 -c 0.90 -g 1</td>
</tr>
<tr>
<td>OLC assembly<br>(asm)</td>
<td>tgicl</td>
<td>2.1</td>
<td style="font-family: Courier New">tgicl <input.fa> -l 60 -p 96 -s 100000</td>
</tr>
<tr>
<td rowspan="5">Cleaning<br>(post_asm)</td>
<td rowspan="2">TransDecoder</td>
<td rowspan="2">2.0.1</td>
<td style="font-family: Courier New">TransDecoder.LongOrfs -t <input.fa></td>
</tr>
<tr>
<td style="font-family: Courier New">TransDecoder.Predict -t <input.fa></td>
</tr>
<tr>
<td>bedtools</td>
<td>2.22.1</td>
<td style="font-family: Courier New">bedtools merge -c 4 -o distinct -i -</td>
</tr>
<tr>
<td>NCBI tools</td>
<td>6.1</td>
<td style="font-family: Courier New">vecscreen -i <input.fa> -d <database.fa> -f 3</td>
</tr>
<tr>
<td>EMBOSS</td>
<td>6.4.0.0</td>
<td style="font-family: Courier New">getorf -auto -filter</td>
</tr>
<tr>
<td rowspan="3">Editing by reads alignment<br>(rmbt_editing)</td>
<td>bwa</td>
<td>0.7.12</td>
<td style="font-family: Courier New">bwa [aln|sampe|samse]</td>
</tr>
<tr>
<td>STAR</td>
<td>2.4.0i</td>
<td style="font-family: Courier New">STAR --genomeDir <dir> --readFilesIn <R1.fq> <R2.fq> --alignIntronMin 10 --alignIntronMax 25000 --outFilterMultimapNmax 10000</td>
</tr>
<tr>
<td>samtools</td>
<td>1.1</td>
<td style="font-family: Courier New">samtools [mpileup|sort|index|flagstat|view|merge|faidx]</td>
</tr>
<tr>
<td>Filtering by reads alignment<br>(rmbt_filtering)</td>
<td>eXpress</td>
<td>1.5.1</td>
<td style="font-family: Courier New">express --no-update-check --no-bias-correct --logtostderr --output-dir <outdir> <reference.fa> <input.bam></td>
</tr>
<tr>
<td>Scoring<br>(postprocess)</td>
<td>TransRate</td>
<td>1.0.1</td>
<td style="font-family: Courier New">transrate --assembly=<input.fa> --left=<R1.fq> --right=<R2.fq> --threads=%d --output=<outdir></td>
</tr>
<tr>
<td rowspan="2">Reference alignment<br>(reference)</td>
<td>Exonerate</td>
<td>2.2.0</td>
<td style="font-family: Courier New">exonerate --percent 50 --verbose 0 --showalignment no --showvulgar no <queries.fa> <targets.fa></td>
</tr>
<tr>
<td>Blat</td>
<td>BlatSuite v34</td>
<td style="font-family: Courier New">blat <targets.fa> <queries.fa> -noHead <output.psl></td>
</tr>
</tbody>
</table>
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