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SEECER: SEquencing Error CorrEction for Rna-Seq data
Probabilistic error correction in de novo RNA sequencing
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Hai-Son Le (hple@cs.cmu.edu)
Marcel Schulz (maschulz@cs.cmu.edu)
Ziv Bar-Joseph (zivbj@cs.cmu.edu)
Requirements:
1. JELLYFISH
2. SeqAn
3. GNU Scientific Library
Installation:
1. Compile JELLYFISH
cd jellyfish-1.1.4/
./configure
make
2. Compile SEECER:
cd SEECER
./configure
make
3. Usage:
+ Bash script to run Seecer:
# This script runs the SEECER pipeline of 4 steps:
#
# 1. Replace Ns and strip off read IDs (to save memory).
# 2. Run JellyFish to count kmers.
# 3. Correct errors with SEECER.
# 4. Clean up and put back original read IDs.
run_seecer.sh [options] read1 read2
read1, read2: are Fasta/Fastaq files.
If only read1 is provided, the reads are considered singles.
Otherwise, read1 and read2 are paired-end reads.
Options:
-t <v> : *required* specify a temporary working directory.
-k <v> : sepcify a different K value (default = 17).
-j <v> : specify the location of JELLYFISH binary
(default = ../jellyfish-1.1.4/bin/jellyfish).
-p <v> : specify extra SEECER parameters (default = '').
-s <v> : specify the starting step ( default = 1). Values = 1,2,3,4.
-h : help message
+ Seecer's parameters:
# seecer [options] read1 [read2]
# --------------------------------------------
# read1, read2: are Fasta/Fastaq files.
# If only read1 is provided, the reads are considered singles.
# Otherwise, read1 and read2 are paired-end reads.
# *** Important ***:
# Reads should not contain Ns. Please use the provided run_seecer.sh
# script to handle Ns.
# --------------------------------------------
# Options:
# --kmer <k> : specify a different K value (default = 17).
# --kmerCount <f> : specify the file containing kmer counts. This file
# is produced by JELLYFISH, we provided a Bash script to generate this file
# (run_seecer.sh).
# If the parameter is not set, SEECER will count kmers by itself
# (slower and memory-inefficient).
# --clusterLLH <e> : specify a different log likelihood threshold (default = -1).
# --entropy <e> : specify a different entropy threshold (default = 0.6).
# --help, -h : this help message.
4. Test cases:
* Small dataset
(first 25000 pairs of SRR027877 from www.ncbi.nlm.nih.gov/sra/SRX011546)
bash ./bin/run_seecer.sh testdata/SRR027877-small-p1.fastq testdata/SRR027877-small-p2.fastq
The corrected reads are store in the files testdata/*_corrected.fa
Licenses:
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.