Commit da78492c authored by Lucile Broseus's avatar Lucile Broseus

Update README.md

parent 045c5e7a
**TALC: Transcriptome-Aware Long Read Correction**
TALC is an hybrid Long Read correction method tailored for RNA-seq data.
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**Requirements:**
*
* Jellyfish2
Currently, TALC makes use of k-mer counts table as dumped by the Jellyfish2 k-mer counter.
Currently, TALC makes use of k-mer counts table as dumped by Jellyfish2.
Jellyfish2 can be dowload from: https://github.com/zippav/Jellyfish-2
Jellyfish2 can be dowload from: https://github.com/zippav/Jellyfish-2.
Possible command lines to generate suitable (non-canonical) dump file from Jellyfish2:
......@@ -25,7 +29,11 @@ jellyfish count --mer $kmerSize -s 100M -o $out.jf -t $nthreads $SRfq
jellyfish dump -c $out.jf > $out.dump
```
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* Adapter trimming
Adapter sequences should be removed from all datasets before running TALC correction.
No additional filtering is needed.
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**Running TALC**
......@@ -54,3 +62,10 @@ talc $LReads \ # File containg the long reads, in fasta of fastq forma
-o $out \ # Prefix for the output
-t $num_threads # Number of threads
```
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**Dependencies**
TALC is built upon the SeqAn2 C++ library.
https://github.com/seqan/seqan
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